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<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>Sorry if this mail was duplicated... I think I have sent it by error to <A href="mailto:gmx-usres-requsts@gromacs.org">gmx-usres-requsts@gromacs.org</A></FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3></FONT></SPAN> </P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>Dear Gromacs community,</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>I’m running MD simulation for ligand-enzyme complex with the help of the great tutorial set by Kerrigan using version 3.3.1.</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>In certain stage of my simulation I need to fix the position of some residues in the enzyme. In order to do so I thought about two options for doing that:</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3> </FONT></SPAN></P>
<OL type=1>
<LI class=EC_MsoNormal style="tab-stops: list 36.0pt"><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>The first is by the use of “<I>freezegrps</I>” where I have generated and .ndx (IRS.ndx) file for the residues to be frozen and I have modified my .mdp file to be:</FONT></SPAN></LI></OL>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3> </FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>title<SPAN> </SPAN>= dynamic for 2zd1</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>cpp<SPAN> </SPAN>= /usr/bin/cpp</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>integrator<SPAN> </SPAN>= md</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000><STRONG>constraints<SPAN> </SPAN>= none</STRONG></FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>dt<SPAN> </SPAN>= 0.002</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>nsteps<SPAN> </SPAN>= 500000<SPAN> </SPAN>; total 1 ns.</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>nstcomm<SPAN> </SPAN><SPAN> </SPAN>= 1</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>nstxout<SPAN> </SPAN>= 5000</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>nstvout<SPAN> </SPAN>= 0</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>nstfout<SPAN> </SPAN>= 0</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>nstlist<SPAN> </SPAN>= 10</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>ns_type<SPAN> </SPAN>= grid</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>rlist<SPAN> </SPAN>= 1</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>coulombtype<SPAN> </SPAN>= PME</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>rcoulomb<SPAN> </SPAN>= 1</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>vdwtype<SPAN> </SPAN>= cut-off</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>rvdw<SPAN> </SPAN>= 1.4</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>fourierspacing<SPAN> </SPAN>= 0.12</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>fourier_nx<SPAN> </SPAN>= 0</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>fourier_ny<SPAN> </SPAN>= 0</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>fourier_nz<SPAN> </SPAN>= 0</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>pme_order<SPAN> </SPAN>= 6</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>ewald_rtol<SPAN> </SPAN><SPAN> </SPAN>= 1e-5</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>optimize_fft<SPAN> </SPAN>= yes</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>Tcoupl<SPAN> </SPAN>= berendsen</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>tau_t<SPAN> </SPAN>= 0.1 0.1 0.1 0.1</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>tc_grps<SPAN> </SPAN>= protein T27 SOL Cl ; T27 is the ligand</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>ref_t<SPAN> </SPAN>= 300 300 300 300</FONT></SPAN></P>
<P class=EC_MsoNormal><FONT color=#000000><B><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'">energygrps<SPAN> </SPAN>= protein T27 SOL </SPAN></B><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"></SPAN></FONT></P>
<P class=EC_MsoNormal><B><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>energygrp_excl<SPAN> </SPAN>= IRS IRS IRS SOL</FONT></SPAN></B></P>
<P class=EC_MsoNormal><B><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>freezegrps<SPAN> </SPAN>= IRS</FONT></SPAN></B></P>
<P class=EC_MsoNormal><B><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>freezedim<SPAN> </SPAN>= Y Y Y</FONT></SPAN></B></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>Pcoupl<SPAN> </SPAN>= berendsen</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>pcoupltype<SPAN> </SPAN>= isotropic</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>tau_p<SPAN> </SPAN>= 0.5</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>compressibility<SPAN> </SPAN>= 4.5e-5</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>ref_p<SPAN> </SPAN><SPAN> </SPAN>= 1.0</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>gen_vel<SPAN> </SPAN>= yes</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>gen_temp<SPAN> </SPAN>= 300</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'"><FONT color=#000000>gen_seed<SPAN> </SPAN>= 173529</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3> </FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>and when I used the grommp line of </FONT></SPAN></P>
<P class=EC_MsoNormal><FONT size=3><FONT color=#000000><FONT face="Times New Roman"><B><SPAN lang=EN-AU>grompp</SPAN></B><SPAN lang=EN-AU> -f md.mdp -c 2zd1_eq.gro -p 2zd1.top -n IRS.ndx -o md.tpr</SPAN></FONT></FONT></FONT></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>I had (as expected) an error massage states that IRS is not an energy group however if I have added IRS as an energy group I had an error that some atoms are in multiple energy Mon. groups.</FONT></SPAN></P>
<P class=EC_MsoNormal><B><SPAN lang=EN-AU><FONT size=3><FONT color=#000000><FONT face="Times New Roman">So, my first question is how to deal with that problem for including my frozen residues that way?</FONT></FONT></FONT></SPAN></B></P>
<P class=EC_MsoNormal><B><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3> </FONT></SPAN></B></P>
<P class=EC_MsoNormal><FONT size=3><FONT color=#000000><FONT face="Times New Roman"><SPAN>2<STRONG>.</STRONG> The second method I think about is to just position-restrained these residues where I have created an .itp file for the residues need to be fixed (POSRE_IRS.itp) using<EM> genpr </EM>command. But I don’t know how to consider that in the calculations…. </SPAN></FONT></FONT></FONT></P>
<P class=EC_MsoNormal><B><SPAN lang=EN-AU><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Can I just include this file in the toplogy file (#include “POSRE_IRS.itp”) and add the line Define = -DPOSRE_IRS in my .mdp file??</FONT></FONT></FONT></SPAN></B></P>
<P class=EC_MsoNormal><B><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3> </FONT></SPAN></B></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>Looking forward for your kind suggestions and comments</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3> </FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>Great Thanks</FONT></SPAN></P>
<P class=EC_MsoNormal><SPAN lang=EN-AU><FONT face="Times New Roman" color=#000000 size=3>Mohammed </FONT></SPAN></P><BR>
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