Justin, <br><br>Regarding the charges you mention, what do you think about RESP charges for this kind of compounds (drugs) parameterization?<br><br>Best wishes<br><br>Esteban<br><br>--<br><div class="gmail_quote">On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Just the $0.02 that I always seem to contribute in these types of discussions - the topology you have shown below contains some likely problems. The charges (and massive charge group size) can lead to artifacts. We've got a paper due out soon about the implications of incorrect charges, but I would advise you that this topology should *not* be used for production simulation. You'd be better off spending the time to properly parameterize the molecule rather than run a bunch of simulations and get questionable (at best) or wrong (at worst) results.<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
-Justin<br>
<br>
Olga Ivchenko wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
Hey Vitaly,<br>
<br>
Thank you for your reply. Here is the files:<br>
<br>
*itp:*<br>
; ; ; This file was generated by PRODRG version AA081006.0504<br>
; PRODRG written/copyrighted by Daan van Aalten<br>
; and Alexander Schuettelkopf<br></div>
; ; Questions/comments to <a href="mailto:dava@davapc1.bioch.dundee.ac.uk" target="_blank">dava@davapc1.bioch.dundee.ac.uk</a> <mailto:<a href="mailto:dava@davapc1.bioch.dundee.ac.uk" target="_blank">dava@davapc1.bioch.dundee.ac.uk</a>><div>
<div></div><div class="h5"><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>
[ 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 2 C 1 DRG C 1 0.402 12.0110 3 OM 1 DRG O 1 -0.701 15.9994 4 CH2 1 DRG CA 2 0.185 14.0270 5 N 1 DRG N 2 0.468 14.0067 6 CH3 1 DRG CAG 2 0.201 15.0350 7 C 1 DRG CAH 2 0.377 12.0110 8 NZ 1 DRG NAE 2 -0.163 14.0067 9 H 1 DRG HA6 2 0.023 1.0080 10 H 1 DRG HAE 2 0.024 1.0080 11 NZ 1 DRG NAD 2 -0.163 14.0067 12 H 1 DRG HA5 2 0.024 1.0080 13 H 1 DRG HAD 2 0.024 1.0080 <br>
[ bonds ]<br>
; ai aj fu c0, c1, ...<br>
2 1 2 0.125 13400000.0 0.125 13400000.0 ; C OXT 2 3 2 0.125 13400000.0 0.125 13400000.0 ; C O 2 4 2 0.153 7150000.0 0.153 7150000.0 ; C CA 5 4 2 0.147 8710000.0 0.147 8710000.0 ; N CA 5 6 2 0.147 8710000.0 0.147 8710000.0 ; N CAG 5 7 2 0.134 10500000.0 0.134 10500000.0 ; N CAH 7 8 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAE 7 11 2 0.134 10500000.0 0.134 10500000.0 ; CAH NAD 8 9 2 0.100 18700000.0 0.100 18700000.0 ; NAE HA6 8 10 2 0.100 18700000.0 0.100 18700000.0 ; NAE HAE 11 12 2 0.100 18700000.0 0.100 18700000.0 ; NAD HA5 11 13 2 0.100 18700000.0 0.100 18700000.0 ; NAD HAD <br>
[ pairs ]<br>
; ai aj fu c0, c1, ...<br>
1 5 1 ; OXT N 2 6 1 ; C CAG 2 7 1 ; C CAH 3 5 1 ; O N 4 8 1 ; CA NAE 4 11 1 ; CA NAD 5 9 1 ; N HA6 5 10 1 ; N HAE 5 12 1 ; N HA5 5 13 1 ; N HAD 6 8 1 ; CAG NAE 6 11 1 ; CAG NAD 8 12 1 ; NAE HA5 8 13 1 ; NAE HAD 9 11 1 ; HA6 NAD 10 11 1 ; HAE NAD <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 1 2 4 2 117.0 635.0 117.0 635.0 ; OXT C CA 3 2 4 2 117.0 635.0 117.0 635.0 ; O C CA 2 4 5 2 109.5 520.0 109.5 520.0 ; C CA N 4 5 6 2 121.0 685.0 121.0 685.0 ; CA N CAG 4 5 7 2 122.0 700.0 122.0 700.0 ; CA N CAH 6 5 7 2 117.0 635.0 117.0 635.0 ; CAG N CAH 5 7 8 2 120.0 670.0 120.0 670.0 ; N CAH NAE 5 7 11 2 120.0 670.0 120.0 670.0 ; N CAH NAD 8 7 11 2 120.0 670.0 120.0 670.0 ; NAE CAH NAD 7 8 9 2 120.0 390.0 120.0 390.0 ; CAH NAE HA6 7 8 10 2 120.0 390.0 120.0 390.0 ; CAH NAE HAE 9 8 10 2 120.0 445.0 120.0 445.0 ; HA6 NAE HAE 7 11 12 2 120.0 390.0 120.0 390.0 ; CAH NAD HA5 7 11 13 2 120.0 390.0 120.0 390.0 ; CAH NAD HAD 12 11 13 2 120.0 445.0 120.0 445.0 ; HA5 NAD HAD <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 5 4 6 7 2 0.0 167.4 0.0 167.4 ; imp N CA CAG CAH 7 5 8 11 2 0.0 167.4 0.0 167.4 ; imp CAH N NAE NAD 8 7 10 9 2 0.0 167.4 0.0 167.4 ; imp NAE CAH HAE HA6 11 7 13 12 2 0.0 167.4 0.0 167.4 ; imp NAD CAH HAD HA5 5 4 2 1 1 0.0 1.0 6 0.0 1.0 6 ; dih N CA C OXT 2 4 5 7 1 180.0 1.0 6 180.0 1.0 6 ; dih C CA N CAH 11 7 5 4 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD CAH N CA 5 7 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH NAE HAE 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>
*And top. I am prettu sure this file is wrong. And I do not know yet how to modify it correctly:<br>
<br>
*<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></div>
2010/11/15 Vitaly Chaban <<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a> <mailto:<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>>><div class="im"><br>
<br>
Hey, Olga -<br>
<br>
> Also please can you tell me where can I get "ffgmx.itp" file?<br>
<br>
/$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other<br>
standard topology files are there.<br>
<br>
By trying to run md I am getting an error: Fatal error:<br>
> moleculetype UNK is redefined<br>
<br>
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>
<br>
Vitaly<br>
<br>
<br>
<br>
<br>
> I still have troubles of starting running md for creatine. For<br>
which I<br>
> created topology using PRODRG programm.<br>
> The only difference between creatine.top and creating.itp is that<br>
creatine<br>
> top has additional lines:<br>
> #include "ffgmx.itp"<br>
> #include "creatine.itp"<br>
><br>
> Also please can you tell me where can I get "ffgmx.itp" file?<br>
><br>
> By trying to run md I am getting an error: Fatal error:<br>
> moleculetype UNK is redefined<br>
<br>
<br>
</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div><div></div><div class="h5"><br>
-- <br>
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</div></div></blockquote></div><br>