<br>Hey Vitaly,<br><br>Thank you for your reply. Here is the files: <br><br><b>itp:</b><br>; <br>; <br>; This file was generated by PRODRG version AA081006.0504<br>; PRODRG written/copyrighted by Daan van Aalten<br>
; and Alexander Schuettelkopf<br>; <br>; Questions/comments to <a href="mailto:dava@davapc1.bioch.dundee.ac.uk">dava@davapc1.bioch.dundee.ac.uk</a><br>; <br>; When using this software in a publication, cite:<br>
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).<br>; PRODRG - a tool for high-throughput crystallography<br>; of protein-ligand complexes.<br>; Acta Crystallogr. D60, 1355--1363.<br>; <br>
; <br><br>[ moleculetype ]<br> Name nrexcl<br>DRG 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 OM 1 DRG OXT 1 -0.701 15.9994 <br> 2 C 1 DRG C 1 0.402 12.0110 <br>
3 OM 1 DRG O 1 -0.701 15.9994 <br> 4 CH2 1 DRG CA 2 0.185 14.0270 <br> 5 N 1 DRG N 2 0.468 14.0067 <br> 6 CH3 1 DRG CAG 2 0.201 15.0350 <br>
7 C 1 DRG CAH 2 0.377 12.0110 <br> 8 NZ 1 DRG NAE 2 -0.163 14.0067 <br> 9 H 1 DRG HA6 2 0.023 1.0080 <br> 10 H 1 DRG HAE 2 0.024 1.0080 <br>
11 NZ 1 DRG NAD 2 -0.163 14.0067 <br> 12 H 1 DRG HA5 2 0.024 1.0080 <br> 13 H 1 DRG HAD 2 0.024 1.0080 <br><br>[ bonds ]<br>; ai aj fu c0, c1, ...<br>
2 1 2 0.125 13400000.0 0.125 13400000.0 ; C OXT <br> 2 3 2 0.125 13400000.0 0.125 13400000.0 ; C O <br> 2 4 2 0.153 7150000.0 0.153 7150000.0 ; C CA <br>
5 4 2 0.147 8710000.0 0.147 8710000.0 ; N CA <br> 5 6 2 0.147 8710000.0 0.147 8710000.0 ; N CAG <br> 5 7 2 0.134 10500000.0 0.134 10500000.0 ; N CAH <br>
7 8 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAE <br> 7 11 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAD <br> 8 9 2 0.100 18700000.0 0.100 18700000.0 ; NAE HA6 <br>
8 10 2 0.100 18700000.0 0.100 18700000.0 ; NAE HAE <br> 11 12 2 0.100 18700000.0 0.100 18700000.0 ; NAD HA5 <br> 11 13 2 0.100 18700000.0 0.100 18700000.0 ; NAD HAD <br>
<br>[ pairs ]<br>; ai aj fu c0, c1, ...<br> 1 5 1 ; OXT N <br> 2 6 1 ; C CAG <br> 2 7 1 ; C CAH <br>
3 5 1 ; O N <br> 4 8 1 ; CA NAE <br> 4 11 1 ; CA NAD <br>
5 9 1 ; N HA6 <br> 5 10 1 ; N HAE <br> 5 12 1 ; N HA5 <br>
5 13 1 ; N HAD <br> 6 8 1 ; CAG NAE <br> 6 11 1 ; CAG NAD <br>
8 12 1 ; NAE HA5 <br> 8 13 1 ; NAE HAD <br> 9 11 1 ; HA6 NAD <br>
10 11 1 ; HAE NAD <br><br>[ angles ]<br>; ai aj ak fu c0, c1, ...<br> 1 2 3 2 126.0 770.0 126.0 770.0 ; OXT C O <br> 1 2 4 2 117.0 635.0 117.0 635.0 ; OXT C CA <br>
3 2 4 2 117.0 635.0 117.0 635.0 ; O C CA <br> 2 4 5 2 109.5 520.0 109.5 520.0 ; C CA N <br> 4 5 6 2 121.0 685.0 121.0 685.0 ; CA N CAG <br>
4 5 7 2 122.0 700.0 122.0 700.0 ; CA N CAH <br> 6 5 7 2 117.0 635.0 117.0 635.0 ; CAG N CAH <br> 5 7 8 2 120.0 670.0 120.0 670.0 ; N CAH NAE <br>
5 7 11 2 120.0 670.0 120.0 670.0 ; N CAH NAD <br> 8 7 11 2 120.0 670.0 120.0 670.0 ; NAE CAH NAD <br> 7 8 9 2 120.0 390.0 120.0 390.0 ; CAH NAE HA6 <br>
7 8 10 2 120.0 390.0 120.0 390.0 ; CAH NAE HAE <br> 9 8 10 2 120.0 445.0 120.0 445.0 ; HA6 NAE HAE <br> 7 11 12 2 120.0 390.0 120.0 390.0 ; CAH NAD HA5 <br>
7 11 13 2 120.0 390.0 120.0 390.0 ; CAH NAD HAD <br> 12 11 13 2 120.0 445.0 120.0 445.0 ; HA5 NAD HAD <br><br>[ dihedrals ]<br>; ai aj ak al fu c0, c1, m, ...<br>
2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp C OXT O CA <br> 5 4 6 7 2 0.0 167.4 0.0 167.4 ; imp N CA CAG CAH <br> 7 5 8 11 2 0.0 167.4 0.0 167.4 ; imp CAH N NAE NAD <br>
8 7 10 9 2 0.0 167.4 0.0 167.4 ; imp NAE CAH HAE HA6 <br> 11 7 13 12 2 0.0 167.4 0.0 167.4 ; imp NAD CAH HAD HA5 <br> 5 4 2 1 1 0.0 1.0 6 0.0 1.0 6 ; dih N CA C OXT <br>
2 4 5 7 1 180.0 1.0 6 180.0 1.0 6 ; dih C CA N CAH <br> 11 7 5 4 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD CAH N CA <br> 5 7 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH NAE HAE <br>
5 7 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH NAD HAD <br><br><br><br><br><br><br><br><br><b>And top. I am prettu sure this file is wrong. And I do not know yet how to modify it correctly:<br>
<br></b><br><br>;<br>; File 'creatine.top' was generated<br>; By user: onbekend (0)<br>; On host: onbekend<br>; At date: Mon Nov 15 13:24:44 2010<br>;<br>; This is your topology file<br>; it was generated using program:<br>
; pdb2gmx - version 4.5-beta2<br>; with command line:<br>; pdb2gmx -f creatine_all_hyd_PRODRGBeta.pdb -o creatine.gro -p creatine.top <br>;<br><br>#include "creatine.itp"<br>#include "gromos43a1.ff"<br>
<br><br>; Include forcefield parameters<br>;#include "gromos43a1.ff/forcefield.itp"<br><br>;"gromos43a1.ff/creatine.itp"<br><br><br>;[ system ]<br><br>;[ molecules ]<br>;DRG 3<br><br><br><br><br><div class="gmail_quote">
2010/11/15 Vitaly Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hey, Olga -<br>
<div class="im"><br>
> Also please can you tell me where can I get "ffgmx.itp" file?<br>
<br>
</div>/$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other<br>
standard topology files are there.<br>
<div class="im"><br>
By trying to run md I am getting an error: Fatal error:<br>
> moleculetype UNK is redefined<br>
<br>
</div>Please post you top and itp files here. Looks like you have 2 creatine<br>
molecules in your topology right now.<br>
<br>
Good luck!<br>
<font color="#888888"><br>
Vitaly<br>
</font><div class="im"><br>
<br>
<br>
<br>
> I still have troubles of starting running md for creatine. For which I<br>
> created topology using PRODRG programm.<br>
> The only difference between creatine.top and creating.itp is that creatine<br>
> top has additional lines:<br>
> #include "ffgmx.itp"<br>
> #include "creatine.itp"<br>
><br>
</div><div class="im">> Also please can you tell me where can I get "ffgmx.itp" file?<br>
><br>
</div><div><div></div><div class="h5">> By trying to run md I am getting an error: Fatal error:<br>
> moleculetype UNK is redefined<br>
</div></div></blockquote></div><br>