<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:14pt"><div><span>Hello,</span></div><div><span></span> </div><div><span>I'm trying to build a box with nbutanol using the residue below for nbutanol (But), added in ffoplsaa.rtp</span></div><div><span></span> </div><div><span><font size="3">; Butanol<br>[ But ] <br>[ atoms ]<br>; <br> C1 opls_135 -0.18 1 <br> H11 opls_140 0.06 1 <br> H12
opls_140 0.06 1 <br> H13 opls_140 0.06 1 <br> C2 opls_136 -0.12 2 <br> H21 opls_140 0.06 2 <br> H22 opls_140 0.06 2 <br> C3 opls_136 -0.12 3 <br> H31 opls_140 0.06 3 <br> H32 opls_140 0.06 3 <br>
C4 opls_157 0.145 4 <br> H41 opls_140 0.06 4 <br> H42 opls_140 0.06 4 <br> OH opls_154 -0.683 4 <br> HO opls_155 0.418 4 </font></span></div><div><span><font size="3">[ bonds ]<br>; ai aj funct c0 c1 c2
c3<br> C1 H11 <br> C1 H12 <br> C1 H13 <br> C1 C2 <br> C2 H21 <br> C2 H22 <br> C2 C3 <br> C3 H31 <br> C3 H32 <br> C3 C4 <br> C4 H41 <br> C4 H42 <br> C4 OH <br> OH HO </font></span></div><div><span><font size="3">[ angles ]<br>; ai aj ak funct c0
c1 c2 c3<br> H11 C1 H12 <br> H11 C1 H13 <br> H11 C1 C2 <br> H12 C1 H13 <br> H12 C1 C2 <br> H13 C1 C2 <br> C1 C2 H21 <br> C1 C2 H22 <br> C1 C2 C3 <br> H21
C2 H22 <br> H21 C2 C3 <br> H22 C2 C3 <br> C2 C3 H31 <br> C2 C3 H32 <br> C2 C3 C4 <br> H31 C3 H32 <br> H31 C3 C4 <br> H32 C3 C4 <br> C3 C4 H41 <br> C3 C4 H42 <br> C3
C4 OH <br> H41 C4 H42 <br> H41 C4 OH <br> H42 C4 OH <br> C4 OH HO </font></span></div><div><span><font size="3">[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4
c5<br> H11 C1 C2 H21 <br> H11 C1 C2 H22 <br> H11 C1 C2 C3 <br> H12 C1 C2 H21 <br> H12 C1 C2 H22 <br> H12 C1 C2 C3 <br> H13 C1 C2 H21 <br> H13 C1 C2 H22 <br> H13 C1 C2 C3 <br> C1 C2 C3 H31 <br> C1 C2 C3 H32
<br> C1 C2 C3 C4 <br> H21 C2 C3 H31 <br> H21 C2 C3 H32 <br> H21 C2 C3 C4 <br> H22 C2 C3 H31 <br> H22 C2 C3 H32 <br> H22 C2 C3 C4 <br> C2 C3 C4 H41 <br> C2 C3 C4 H42 <br> C2 C3 C4 OH <br> H31 C3
C4 H41 <br> H31 C3 C4 H42 <br> H31 C3 C4 OH <br> H32 C3 C4 H41 <br> H32 C3 C4 H42 <br> H32 C3 C4 OH <br> C3 C4 OH HO <br> H41 C4 OH HO <br> H42 C4 </font></span><span><font size="3"> OH HO <br></font></div></span><div>The .gro file used is</div><div><font size="3">15<br> 1But C1 1 2.561
2.686 0.006<br> 1But H11 2 2.470 2.721 -0.042<br> 1But H12 3 2.576 2.582 -0.021<br> 1But H13 4 2.544 2.690 0.114<br> 1But C2 5 2.681 2.772 -0.034<br> 1But H21 6 2.692 2.769 -0.143<br> 1But H22 7 2.661 2.877 -0.008<br> 1But C3 8 2.811 2.727 0.033<br> 1But H31 9 2.799 2.730 0.141<br> 1But H32 10 2.831 2.623 0.007<br> 1But C4 11 2.932 2.813 -0.008<br> 1But H41 12
2.947 2.810 -0.116<br> 1But H42 13 2.916 2.917 0.020<br> 1But OH 14 3.048 2.765 0.055<br> 1But HO 15 3.122 2.816 0.026<br> 2.75000 2.75000 2.75000</font></div><div> </div><div>The command line for obtaining the topology file: </div><div> </div><div>pdb2gmx -f nbutoh.gro -o nbutoh2.gro -p topol.top<br></div><div>return the error message:</div><div> </div><div><font size="3">Fatal error:<br>Invalid line in nbutoh.gro for atom 1:<br> 1But C1 1 2.561 2.686 0.006<br></font></div><div>I have tried of different ways for obtaining the gro and the topology file, include using the pdb file below, but<span class="hps"> it still
fails.</span></div><div> </div><div> </div><div><font size="3">HETATM 1 C1 But 1 2.510 -0.293 0.000<br>HETATM 2 H11 But 1 3.385 0.351 -0.000<br>HETATM 3 H12 But 1 2.567 -0.931 0.878<br>HETATM 4 H13 But 1 2.567 -0.931 -0.878<br>HETATM 5 C2 But 1 1.222 0.528 -0.000<br>HETATM
6 H21 But 1 1.212 1.180 0.871<br>HETATM 7 H22 But 1 1.212 1.180 -0.871<br>HETATM 8 C3 But 1 -0.036 -0.341 -0.000<br>HETATM 9 H31 But 1 -0.041 -0.990 -0.873<br>HETATM 10 H32 But 1 -0.041 -0.990 0.873<br>HETATM 11 C4 But 1 -1.317
0.471 0.000<br>HETATM 12 H41 But 1 -1.349 1.113 0.880<br>HETATM 13 H42 But 1 -1.349 1.113 -0.880<br>HETATM 14 OH But 1 -2.404 -0.419 0.000<br>HETATM 15 HO Bu t 1 -3.209 0.066 0.000<br>CONECT 1 2 3 4 5<br>CONECT 2 1<br>CONECT 3 1<br>CONECT 4
1<br>CONECT 5 1 6 7 8<br>CONECT 6 5<br>CONECT 7 5<br>CONECT 8 5 9 10 11<br>CONECT 9 8<br>CONECT 10 8<br>CONECT 11 8 12 13 14<br>CONECT 12 11<br>CONECT 13 11<br>CONECT 14 11 15<br>CONECT 15 14<br>END</font></div><div><font size="3"></font> </div><div><font size="4">Can you help me to solve my problem?</font></div><div><font size="4"></font> </div><div><font size="4">Thanks,</font></div><div> <var id="yui-ie-cursor"></var></div><div>-- <br>Juliana Angeiras Batista da
Silva<br>Laboratório de Química Teórica e Computacional<br>Departamento de Química Fundamental<br>Universidade Federal de Pernambuco<br>50740-540 Recife (PE) - Brazil<br><br></div><div>Phone: +55 81 2126-8440 ext. 5007<br>Phone: +55 81 9197-9297.</div></div></body></html>