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<P><FONT face="times new roman, new york, times, serif">Dear all,</FONT></P>
<P> </P>
<P><FONT face="times new roman, new york, times, serif">Sorry for the previous e-mail format. </FONT><FONT face="times new roman, new york, times, serif">I am writing again the problem.</FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif">I am trying to simulate drug at the binding site of the receptor surrounded by DPPC bilayer system. I have problem at the energy minimisation step. Always, I am getting below error message:</FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif">Warning: 1-4 interaction between 3642 and 3647 at distance 1.325 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file</FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif">Step= 0, Dmax= 1.0e-02 nm, Epot= 7.16584e+15 Fmax= 5.29841e+18, atom= 2662 Step= 1, Dmax= 1.0e-02 nm, Epot= 1.19114e+12 Fmax= 2.10320e+14, atom= 3605 Step= 2, Dmax= 1.2e-02 nm, Epot= 1.39843e+10 Fmax= 8.84756e+11, atom= 2662 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.36040e+09 Fmax= 5.31692e+10, atom= 2661 </FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif">When I try to increase table-extension to more than 1.0, 1-4 interaction always increases.</FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif">I checked the *.gro file, it seems during the minimisation, bonds at protein and drg molecules are fine however, bonds at the DPPC molecules are broken. </FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif">I guess problem is at the *.itp file of dppc. I produced *.itp file of DPPC from PRODRG. *itp file of lipid and *.mdp file for energy minimisation are attached below. Could any body give a clue for the solution? Many thanks in advanced. </FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif">Serdar Durdagi </FONT></P>
<P><BR><FONT face="times new roman, new york, times, serif"> </FONT></P><FONT size=2>
<P><FONT face="times new roman, new york, times, serif">; </FONT></P>
<P><FONT face="times new roman, new york, times, serif">; </FONT></P>
<P><FONT face="times new roman, new york, times, serif">; This file was generated by PRODRG version 071121.0636</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; PRODRG written/copyrighted by Daan van Aalten</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; and Alexander Schuettelkopf</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; </FONT></P>
<P><FONT face="times new roman, new york, times, serif">; Questions/comments to dava@davapc1.bioch.dundee.ac.uk</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; </FONT></P>
<P><FONT face="times new roman, new york, times, serif">; When using this software in a publication, cite:</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; A. W. Schuettelkopf and D. M. F. van Aalten (2004).</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; PRODRG - a tool for high-throughput crystallography</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; of protein-ligand complexes.</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; Acta Crystallogr. D60, 1355--1363.</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; </FONT></P>
<P><FONT face="times new roman, new york, times, serif">; </FONT></P>
<P><FONT face="times new roman, new york, times, serif">[ moleculetype ]</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; Name nrexcl</FONT></P>
<P><FONT face="times new roman, new york, times, serif">MOL 3</FONT></P>
<P><FONT face="times new roman, new york, times, serif">[ atoms ]</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; nr type resnr resid atom cgnr charge mass</FONT></P>
<P><FONT face="times new roman, new york, times, serif">1 CH3 1 MOL C8 1 -0.033 15.0350 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">2 CH2 1 MOL C1 1 0.008 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">3 CH2 1 MOL C45 1 0.008 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">4 CH2 1 MOL C44 1 0.009 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">5 CH2 1 MOL C43 1 0.008 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">6 CH2 1 MOL C42 2 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">7 CH2 1 MOL C41 2 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">8 CH2 1 MOL C40 3 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">9 CH2 1 MOL C39 3 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">10 CH2 1 MOL C38 4 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">11 CH2 1 MOL C37 4 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">12 CH2 1 MOL C36 5 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">13 CH2 1 MOL C35 5 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">14 CH2 1 MOL C34 6 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">15 CH2 1 MOL C33 7 0.036 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">16 C 1 MOL C32 7 0.438 12.0110 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">17 O 1 MOL O46 7 -0.551 15.9994 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">18 OS 1 MOL O31 7 -0.160 15.9994 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 CS1 1 MOL C13 7 0.237 13.0190 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 CH2 1 MOL C12 8 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">21 OS 1 MOL O11 9 -0.256 15.9994 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 P 1 MOL P8 9 0.998 30.9738 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">23 OM 1 MOL O10 9 -0.743 15.9994 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">24 OM 1 MOL O9 9 -0.743 15.9994 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">25 OS 1 MOL O4 9 -0.256 15.9994 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 CH2 1 MOL C3 10 0.041 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">27 CH2 1 MOL C2 10 0.041 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">28 NL 1 MOL N1 10 0.918 14.0067 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">29 CH3 1 MOL C6 11 0.000 15.0350 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">30 CH3 1 MOL C5 11 0.000 15.0350 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">31 CH3 1 MOL C7 12 0.000 15.0350 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">32 CS2 1 MOL C14 13 0.242 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">33 OS 1 MOL O15 13 -0.162 15.9994 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">34 C 1 MOL C16 13 0.437 12.0110 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">35 O 1 MOL O30 13 -0.553 15.9994 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">36 CH2 1 MOL C17 13 0.036 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">37 CH2 1 MOL C18 14 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">38 CH2 1 MOL C19 14 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">39 CH2 1 MOL C20 15 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">40 CH2 1 MOL C21 15 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">41 CH2 1 MOL C22 16 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">42 CH2 1 MOL C23 16 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">43 CH2 1 MOL C24 17 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">44 CH2 1 MOL C25 17 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">45 CH2 1 MOL C26 18 0.000 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">46 CH2 1 MOL C27 19 0.008 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">47 CH2 1 MOL C28 19 0.008 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">48 CH2 1 MOL C29 19 0.008 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">49 CH2 1 MOL C9 19 0.009 14.0270 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">50 CH3 1 MOL C10 19 -0.033 15.0350 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">[ bonds ]</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; ai aj fu c0, c1, ...</FONT></P>
<P><FONT face="times new roman, new york, times, serif">1 2 1 0.153 334720.0 0.153 334720.0 ; C8 C1 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">2 3 1 0.153 334720.0 0.153 334720.0 ; C1 C45 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">3 4 1 0.153 334720.0 0.153 334720.0 ; C45 C44 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">4 5 1 0.153 334720.0 0.153 334720.0 ; C44 C43 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">5 6 1 0.153 334720.0 0.153 334720.0 ; C43 C42 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">6 7 1 0.153 334720.0 0.153 334720.0 ; C42 C41 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">7 8 1 0.153 334720.0 0.153 334720.0 ; C41 C40 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">8 9 1 0.153 334720.0 0.153 334720.0 ; C40 C39 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">9 10 1 0.153 334720.0 0.153 334720.0 ; C39 C38 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">10 11 1 0.153 334720.0 0.153 334720.0 ; C38 C37 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">11 12 1 0.153 334720.0 0.153 334720.0 ; C37 C36 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">12 13 1 0.153 334720.0 0.153 334720.0 ; C36 C35 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">13 14 1 0.153 334720.0 0.153 334720.0 ; C35 C34 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">14 15 1 0.153 334720.0 0.153 334720.0 ; C34 C33 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">15 16 1 0.153 334720.0 0.153 334720.0 ; C33 C32 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">16 17 1 0.123 502080.0 0.123 502080.0 ; C32 O46 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">16 18 1 0.136 376560.0 0.136 376560.0 ; C32 O31 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">18 19 1 0.144 251040.0 0.144 251040.0 ; O31 C13 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 20 1 0.153 251040.0 0.153 251040.0 ; C13 C12 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 32 1 0.152 251040.0 0.152 251040.0 ; C13 C14 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 21 1 0.143 251040.0 0.143 251040.0 ; C12 O11 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">21 22 1 0.161 251040.0 0.161 251040.0 ; O11 P8 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 23 1 0.148 376560.0 0.148 376560.0 ; P8 O10 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 24 1 0.148 376560.0 0.148 376560.0 ; P8 O9 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 25 1 0.161 251040.0 0.161 251040.0 ; P8 O4 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">25 26 1 0.143 251040.0 0.143 251040.0 ; O4 C3 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 27 1 0.153 334720.0 0.153 334720.0 ; C3 C2 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">27 28 1 0.147 376560.0 0.147 376560.0 ; C2 N1 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">28 29 1 0.147 376560.0 0.147 376560.0 ; N1 C6 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">28 30 1 0.147 376560.0 0.147 376560.0 ; N1 C5 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">28 31 1 0.147 376560.0 0.147 376560.0 ; N1 C7 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">32 33 1 0.144 251040.0 0.144 251040.0 ; C14 O15 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">33 34 1 0.136 376560.0 0.136 376560.0 ; O15 C16 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">34 35 1 0.123 502080.0 0.123 502080.0 ; C16 O30 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">34 36 1 0.153 334720.0 0.153 334720.0 ; C16 C17 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">36 37 1 0.153 334720.0 0.153 334720.0 ; C17 C18 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">37 38 1 0.153 334720.0 0.153 334720.0 ; C18 C19 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">38 39 1 0.153 334720.0 0.153 334720.0 ; C19 C20 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">39 40 1 0.153 334720.0 0.153 334720.0 ; C20 C21 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">40 41 1 0.153 334720.0 0.153 334720.0 ; C21 C22 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">41 42 1 0.153 334720.0 0.153 334720.0 ; C22 C23 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">42 43 1 0.153 334720.0 0.153 334720.0 ; C23 C24 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">43 44 1 0.153 334720.0 0.153 334720.0 ; C24 C25 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">44 45 1 0.153 334720.0 0.153 334720.0 ; C25 C26 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">45 46 1 0.153 334720.0 0.153 334720.0 ; C26 C27 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">46 47 1 0.153 334720.0 0.153 334720.0 ; C27 C28 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">47 48 1 0.153 334720.0 0.153 334720.0 ; C28 C29 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">48 49 1 0.153 334720.0 0.153 334720.0 ; C29 C9 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">49 50 1 0.153 334720.0 0.153 334720.0 ; C9 C10 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">[ pairs ]</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; ai aj fu c0, c1, ...</FONT></P>
<P><FONT face="times new roman, new york, times, serif">1 4 1 ; C8 C44 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">2 5 1 ; C1 C43 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">3 6 1 ; C45 C42 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">4 7 1 ; C44 C41 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">5 8 1 ; C43 C40 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">6 9 1 ; C42 C39 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">7 10 1 ; C41 C38 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">8 11 1 ; C40 C37 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">9 12 1 ; C39 C36 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">10 13 1 ; C38 C35 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">11 14 1 ; C37 C34 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">12 15 1 ; C36 C33 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">13 16 1 ; C35 C32 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">14 17 1 ; C34 O46 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">14 18 1 ; C34 O31 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">15 19 1 ; C33 C13 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">16 20 1 ; C32 C12 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">16 32 1 ; C32 C14 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">17 19 1 ; O46 C13 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">18 21 1 ; O31 O11 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">18 33 1 ; O31 O15 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 22 1 ; C13 P8 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 34 1 ; C13 C16 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 23 1 ; C12 O10 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 24 1 ; C12 O9 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 25 1 ; C12 O4 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 33 1 ; C12 O15 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">21 26 1 ; O11 C3 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">21 32 1 ; O11 C14 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 27 1 ; P8 C2 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">23 26 1 ; O10 C3 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">24 26 1 ; O9 C3 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">25 28 1 ; O4 N1 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 29 1 ; C3 C6 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 30 1 ; C3 C5 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 31 1 ; C3 C7 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">32 35 1 ; C14 O30 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">32 36 1 ; C14 C17 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">33 37 1 ; O15 C18 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">34 38 1 ; C16 C19 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">35 37 1 ; O30 C18 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">36 39 1 ; C17 C20 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">37 40 1 ; C18 C21 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">38 41 1 ; C19 C22 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">39 42 1 ; C20 C23 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">40 43 1 ; C21 C24 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">41 44 1 ; C22 C25 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">42 45 1 ; C23 C26 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">43 46 1 ; C24 C27 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">44 47 1 ; C25 C28 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">45 48 1 ; C26 C29 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">46 49 1 ; C27 C9 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">47 50 1 ; C28 C10 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">[ angles ]</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; ai aj ak fu c0, c1, ...</FONT></P>
<P><FONT face="times new roman, new york, times, serif">1 2 3 1 111.0 460.2 111.0 460.2 ; C8 C1 C45 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">2 3 4 1 111.0 460.2 111.0 460.2 ; C1 C45 C44 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">3 4 5 1 111.0 460.2 111.0 460.2 ; C45 C44 C43 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">4 5 6 1 111.0 460.2 111.0 460.2 ; C44 C43 C42 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">5 6 7 1 111.0 460.2 111.0 460.2 ; C43 C42 C41 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">6 7 8 1 111.0 460.2 111.0 460.2 ; C42 C41 C40 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">7 8 9 1 111.0 460.2 111.0 460.2 ; C41 C40 C39 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">8 9 10 1 111.0 460.2 111.0 460.2 ; C40 C39 C38 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">9 10 11 1 111.0 460.2 111.0 460.2 ; C39 C38 C37 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">10 11 12 1 111.0 460.2 111.0 460.2 ; C38 C37 C36 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">11 12 13 1 111.0 460.2 111.0 460.2 ; C37 C36 C35 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">12 13 14 1 111.0 460.2 111.0 460.2 ; C36 C35 C34 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">13 14 15 1 111.0 460.2 111.0 460.2 ; C35 C34 C33 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">14 15 16 1 111.0 460.2 111.0 460.2 ; C34 C33 C32 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">15 16 17 1 121.0 502.1 121.0 502.1 ; C33 C32 O46 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">15 16 18 1 120.0 418.4 120.0 418.4 ; C33 C32 O31 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">17 16 18 1 120.0 418.4 120.0 418.4 ; O46 C32 O31 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">16 18 19 1 109.5 334.7 109.5 334.7 ; C32 O31 C13 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">18 19 20 1 109.5 284.5 109.5 284.5 ; O31 C13 C12 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">18 19 32 1 109.5 284.5 109.5 284.5 ; O31 C13 C14 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 19 32 1 109.5 251.0 109.5 251.0 ; C12 C13 C14 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 20 21 1 111.0 460.2 111.0 460.2 ; C13 C12 O11 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 21 22 1 120.0 397.5 120.0 397.5 ; C12 O11 P8 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">21 22 23 1 109.6 397.5 109.6 397.5 ; O11 P8 O10 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">21 22 24 1 109.6 397.5 109.6 397.5 ; O11 P8 O9 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">21 22 25 1 103.0 397.5 103.0 397.5 ; O11 P8 O4 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">23 22 24 1 120.0 585.8 120.0 585.8 ; O10 P8 O9 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">23 22 25 1 109.6 397.5 109.6 397.5 ; O10 P8 O4 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">24 22 25 1 109.6 397.5 109.6 397.5 ; O9 P8 O4 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 25 26 1 120.0 397.5 120.0 397.5 ; P8 O4 C3 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">25 26 27 1 109.5 460.2 109.5 460.2 ; O4 C3 C2 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 27 28 1 109.5 460.2 109.5 460.2 ; C3 C2 N1 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">27 28 29 1 109.5 376.6 109.5 376.6 ; C2 N1 C6 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">27 28 30 1 109.5 376.6 109.5 376.6 ; C2 N1 C5 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">27 28 31 1 109.5 376.6 109.5 376.6 ; C2 N1 C7 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">29 28 30 1 109.5 376.6 109.5 376.6 ; C6 N1 C5 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">29 28 31 1 109.5 376.6 109.5 376.6 ; C6 N1 C7 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">30 28 31 1 109.5 376.6 109.5 376.6 ; C5 N1 C7 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 32 33 1 109.5 284.5 109.5 284.5 ; C13 C14 O15 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">32 33 34 1 109.5 334.7 109.5 334.7 ; C14 O15 C16 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">33 34 35 1 120.0 418.4 120.0 418.4 ; O15 C16 O30 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">33 34 36 1 120.0 418.4 120.0 418.4 ; O15 C16 C17 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">35 34 36 1 121.0 502.1 121.0 502.1 ; O30 C16 C17 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">34 36 37 1 111.0 460.2 111.0 460.2 ; C16 C17 C18 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">36 37 38 1 111.0 460.2 111.0 460.2 ; C17 C18 C19 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">37 38 39 1 111.0 460.2 111.0 460.2 ; C18 C19 C20 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">38 39 40 1 111.0 460.2 111.0 460.2 ; C19 C20 C21 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">39 40 41 1 111.0 460.2 111.0 460.2 ; C20 C21 C22 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">40 41 42 1 111.0 460.2 111.0 460.2 ; C21 C22 C23 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">41 42 43 1 111.0 460.2 111.0 460.2 ; C22 C23 C24 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">42 43 44 1 111.0 460.2 111.0 460.2 ; C23 C24 C25 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">43 44 45 1 111.0 460.2 111.0 460.2 ; C24 C25 C26 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">44 45 46 1 111.0 460.2 111.0 460.2 ; C25 C26 C27 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">45 46 47 1 111.0 460.2 111.0 460.2 ; C26 C27 C28 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">46 47 48 1 111.0 460.2 111.0 460.2 ; C27 C28 C29 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">47 48 49 1 111.0 460.2 111.0 460.2 ; C28 C29 C9 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">48 49 50 1 111.0 460.2 111.0 460.2 ; C29 C9 C10 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">[ dihedrals ]</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; ai aj ak al fu c0, c1, m, ...</FONT></P>
<P><FONT face="times new roman, new york, times, serif">16 15 18 17 2 0.0 1673.6 0.0 1673.6 ; imp C32 C33 O31 O46 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">34 33 36 35 2 0.0 1673.6 0.0 1673.6 ; imp C16 O15 C17 O30 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 18 32 20 2 35.3 836.8 35.3 836.8 ; imp C13 O31 C14 C12 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 21 24 23 2 35.3 836.8 35.3 836.8 ; imp P8 O11 O9 O10 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">28 27 29 30 2 35.3 836.8 35.3 836.8 ; imp N1 C2 C6 C5 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C44 C45 C1 C8 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih C43 C44 C45 C1 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih C42 C43 C44 C45 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih C41 C42 C43 C44 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C40 C41 C42 C43 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih C39 C40 C41 C42 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih C38 C39 C40 C41 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C37 C38 C39 C40 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C36 C37 C38 C39 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih C35 C36 C37 C38 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; dih C34 C35 C36 C37 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">15 14 13 12 1 0.0 5.9 3 0.0 5.9 3 ; dih C33 C34 C35 C36 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">16 15 14 13 1 0.0 5.9 3 0.0 5.9 3 ; dih C32 C33 C34 C35 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">14 15 16 18 1 0.0 0.4 6 0.0 0.4 6 ; dih C34 C33 C32 O31 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">15 16 18 19 1 180.0 16.7 2 180.0 16.7 2 ; dih C33 C32 O31 C13 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">32 19 18 16 1 0.0 3.8 3 0.0 3.8 3 ; dih C14 C13 O31 C32 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">18 19 20 21 1 0.0 5.9 3 0.0 5.9 3 ; dih O31 C13 C12 O11 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">33 32 19 18 1 0.0 5.9 3 0.0 5.9 3 ; dih O15 C14 C13 O31 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 21 20 19 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O11 C12 C13 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 21 22 25 1 0.0 1.0 3 0.0 1.0 3 ; dih C12 O11 P8 O4 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">20 21 22 25 1 0.0 3.1 2 0.0 3.1 2 ; dih C12 O11 P8 O4 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 25 22 21 1 0.0 1.0 3 0.0 1.0 3 ; dih C3 O4 P8 O11 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 25 22 21 1 0.0 3.1 2 0.0 3.1 2 ; dih C3 O4 P8 O11 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">22 25 26 27 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O4 C3 C2 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">28 27 26 25 1 0.0 5.9 3 0.0 5.9 3 ; dih N1 C2 C3 O4 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">26 27 28 31 1 0.0 3.8 3 0.0 3.8 3 ; dih C3 C2 N1 C7 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">19 32 33 34 1 0.0 3.8 3 0.0 3.8 3 ; dih C13 C14 O15 C16 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">32 33 34 36 1 180.0 16.7 2 180.0 16.7 2 ; dih C14 O15 C16 C17 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">37 36 34 33 1 0.0 0.4 6 0.0 0.4 6 ; dih C18 C17 C16 O15 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">38 37 36 34 1 0.0 5.9 3 0.0 5.9 3 ; dih C19 C18 C17 C16 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">39 38 37 36 1 0.0 5.9 3 0.0 5.9 3 ; dih C20 C19 C18 C17 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">40 39 38 37 1 0.0 5.9 3 0.0 5.9 3 ; dih C21 C20 C19 C18 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">41 40 39 38 1 0.0 5.9 3 0.0 5.9 3 ; dih C22 C21 C20 C19 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">42 41 40 39 1 0.0 5.9 3 0.0 5.9 3 ; dih C23 C22 C21 C20 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">43 42 41 40 1 0.0 5.9 3 0.0 5.9 3 ; dih C24 C23 C22 C21 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">44 43 42 41 1 0.0 5.9 3 0.0 5.9 3 ; dih C25 C24 C23 C22 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">45 44 43 42 1 0.0 5.9 3 0.0 5.9 3 ; dih C26 C25 C24 C23 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">46 45 44 43 1 0.0 5.9 3 0.0 5.9 3 ; dih C27 C26 C25 C24 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">47 46 45 44 1 0.0 5.9 3 0.0 5.9 3 ; dih C28 C27 C26 C25 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">48 47 46 45 1 0.0 5.9 3 0.0 5.9 3 ; dih C29 C28 C27 C26 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">49 48 47 46 1 0.0 5.9 3 0.0 5.9 3 ; dih C9 C29 C28 C27 </FONT></P>
<P><FONT face="times new roman, new york, times, serif">50 49 48 47 1 0.0 5.9 3 0.0 5.9 3 ; dih C10 C9 C29 C28 </FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif"> </FONT></P>
<P><FONT face="times new roman, new york, times, serif">title = vals</FONT></P>
<P><FONT face="times new roman, new york, times, serif">cpp = /usr/bin/cpp</FONT></P>
<P><FONT face="times new roman, new york, times, serif">define = -DFLEXIBLE</FONT></P>
<P><FONT face="times new roman, new york, times, serif">constraints = none</FONT></P>
<P><FONT face="times new roman, new york, times, serif">integrator = steep</FONT></P>
<P><FONT face="times new roman, new york, times, serif">dt = 0.002 ; ps !</FONT></P>
<P><FONT face="times new roman, new york, times, serif">nsteps = 500</FONT></P>
<P><FONT face="times new roman, new york, times, serif">nstlists = 10</FONT></P>
<P><FONT face="times new roman, new york, times, serif">ns_type = grid</FONT></P>
<P><FONT face="times new roman, new york, times, serif">rlist = 1.0</FONT></P>
<P><FONT face="times new roman, new york, times, serif">coulombtype = PME</FONT></P>
<P><FONT face="times new roman, new york, times, serif">rcoulomb = 1.0</FONT></P>
<P><FONT face="times new roman, new york, times, serif">vdwtype = cut-off</FONT></P>
<P><FONT face="times new roman, new york, times, serif">rvdw = 1.0</FONT></P>
<P><FONT face="times new roman, new york, times, serif">fourierspacing = 0.12</FONT></P>
<P><FONT face="times new roman, new york, times, serif">fourier_nx = 0</FONT></P>
<P><FONT face="times new roman, new york, times, serif">fourier_ny = 0</FONT></P>
<P><FONT face="times new roman, new york, times, serif">fourier_nz = 0</FONT></P>
<P><FONT face="times new roman, new york, times, serif">pme_order = 4</FONT></P>
<P><FONT face="times new roman, new york, times, serif">ewald_rtol = 1e-5</FONT></P>
<P><FONT face="times new roman, new york, times, serif">optimize_fft = yes</FONT></P>
<P><FONT face="times new roman, new york, times, serif">;</FONT></P>
<P><FONT face="times new roman, new york, times, serif">; Energy minimizing</FONT></P>
<P><FONT face="times new roman, new york, times, serif">;</FONT></P>
<P><FONT face="times new roman, new york, times, serif">emtol = 100.0</FONT></P>
<P><FONT face="times new roman, new york, times, serif">emsteps = 0.01</FONT></P>
<P><FONT face="Times New Roman"></FONT> </P></FONT></TD></TR></TBODY></TABLE></DIV></DIV></td></tr></table><br>
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