Dear Sir,<br><br>Greetings!<br><br>It may be basic question but it is very important to go further, my doubt is,<br><br>My protein is soluble form with three ligand and two of them are hetatm (FAD and NADPH) i would like study the substrate, hetatm ligand simulation by gromacs. please make clear to understand and how to do my hetatm to pdb file<br>
<br>Thanks in advance <br><br><div class="gmail_quote">On 16 November 2010 04:03, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</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;">
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Today's Topics:<br>
<br>
1. Protein in Electric Field (S. Mohamadi)<br>
2. Re: Re: still can not run md for creatine<br>
(Esteban Gabriel Vega Hissi)<br>
3. Re: Protein in Electric Field (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 16 Nov 2010 07:54:52 +0330<br>
From: "S. Mohamadi" <<a href="mailto:samira.0630@gmail.com">samira.0630@gmail.com</a>><br>
Subject: [gmx-users] Protein in Electric Field<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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<br>
Dear All<br>
<br>
<br>
I want to simulate a protein in Electric Field how can I do that? where<br>
should I start from!<br>
It's very Important for me! Please help me!<br>
<br>
Thanks<br>
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Message: 2<br>
Date: Tue, 16 Nov 2010 03:47:54 -0300<br>
From: Esteban Gabriel Vega Hissi <<a href="mailto:egvega@gmail.com">egvega@gmail.com</a>><br>
Subject: Re: [gmx-users] Re: still can not run md for creatine<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
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<br>
Justin,<br>
<br>
Regarding the charges you mention, what do you think about RESP charges for<br>
this kind of compounds (drugs) parameterization?<br>
<br>
Best wishes<br>
<br>
Esteban<br>
<br>
--<br>
On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<br>
><br>
> Just the $0.02 that I always seem to contribute in these types of<br>
> discussions - the topology you have shown below contains some likely<br>
> problems. The charges (and massive charge group size) can lead to<br>
> artifacts. We've got a paper due out soon about the implications of<br>
> incorrect charges, but I would advise you that this topology should *not* be<br>
> used for production simulation. You'd be better off spending the time to<br>
> properly parameterize the molecule rather than run a bunch of simulations<br>
> 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>
><br>
>><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<br>
>> AA081006.0504<br>
>> ; PRODRG written/copyrighted by Daan van Aalten<br>
>> ; and Alexander Schuettelkopf<br>
>> ; ; Questions/comments to <a href="mailto:dava@davapc1.bioch.dundee.ac.uk">dava@davapc1.bioch.dundee.ac.uk</a><mailto:<br>
>> <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>
>> [ 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<br>
>> C 1 DRG C 1 0.402 12.0110 3 OM 1 DRG<br>
>> O 1 -0.701 15.9994 4 CH2 1 DRG CA 2<br>
>> 0.185 14.0270 5 N 1 DRG N 2 0.468 14.0067<br>
>> 6 CH3 1 DRG CAG 2 0.201 15.0350 7<br>
>> C 1 DRG CAH 2 0.377 12.0110 8 NZ 1 DRG<br>
>> NAE 2 -0.163 14.0067 9 H 1 DRG HA6 2<br>
>> 0.023 1.0080 10 H 1 DRG HAE 2 0.024 1.0080<br>
>> 11 NZ 1 DRG NAD 2 -0.163 14.0067 12<br>
>> H 1 DRG HA5 2 0.024 1.0080 13 H 1 DRG<br>
>> 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<br>
>> 3 2 0.125 13400000.0 0.125 13400000.0 ; C O 2 4 2<br>
>> 0.153 7150000.0 0.153 7150000.0 ; C CA 5 4 2 0.147<br>
>> 8710000.0 0.147 8710000.0 ; N CA 5 6 2 0.147<br>
>> 8710000.0 0.147 8710000.0 ; N CAG 5 7 2 0.134<br>
>> 10500000.0 0.134 10500000.0 ; N CAH 7 8 2 0.134<br>
>> 10500000.0 0.134 10500000.0 ; CAH NAE 7 11 2 0.134<br>
>> 10500000.0 0.134 10500000.0 ; CAH NAD 8 9 2 0.100<br>
>> 18700000.0 0.100 18700000.0 ; NAE HA6 8 10 2 0.100<br>
>> 18700000.0 0.100 18700000.0 ; NAE HAE 11 12 2 0.100<br>
>> 18700000.0 0.100 18700000.0 ; NAD HA5 11 13 2 0.100<br>
>> 18700000.0 0.100 18700000.0 ; NAD HAD<br>
>> [ pairs ]<br>
>> ; ai aj fu c0, c1, ...<br>
>> 1 5 1 ; OXT N 2<br>
>> 6 1 ; C CAG 2 7 1<br>
>> ; C CAH 3 5 1<br>
>> ; O N 4 8 1<br>
>> ; CA NAE 4 11 1<br>
>> ; CA NAD 5 9 1<br>
>> ; N HA6 5 10 1<br>
>> ; N HAE 5 12 1 ; N<br>
>> HA5 5 13 1 ; N HAD<br>
>> 6 8 1 ; CAG NAE 6 11<br>
>> 1 ; CAG NAD 8 12 1<br>
>> ; NAE HA5 8 13 1<br>
>> ; NAE HAD 9 11 1<br>
>> ; HA6 NAD 10 11 1<br>
>> ; 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<br>
>> O 1 2 4 2 117.0 635.0 117.0 635.0 ; OXT C<br>
>> CA 3 2 4 2 117.0 635.0 117.0 635.0 ; O<br>
>> C CA 2 4 5 2 109.5 520.0 109.5 520.0 ; C<br>
>> CA N 4 5 6 2 121.0 685.0 121.0 685.0 ;<br>
>> CA N CAG 4 5 7 2 122.0 700.0 122.0 700.0 ;<br>
>> CA N CAH 6 5 7 2 117.0 635.0 117.0 635.0<br>
>> ; CAG N CAH 5 7 8 2 120.0 670.0 120.0<br>
>> 670.0 ; N CAH NAE 5 7 11 2 120.0 670.0 120.0<br>
>> 670.0 ; N CAH NAD 8 7 11 2 120.0 670.0 120.0<br>
>> 670.0 ; NAE CAH NAD 7 8 9 2 120.0 390.0 120.0<br>
>> 390.0 ; CAH NAE HA6 7 8 10 2 120.0 390.0<br>
>> 120.0 390.0 ; CAH NAE HAE 9 8 10 2 120.0 445.0<br>
>> 120.0 445.0 ; HA6 NAE HAE 7 11 12 2 120.0<br>
>> 390.0 120.0 390.0 ; CAH NAD HA5 7 11 13 2 120.0<br>
>> 390.0 120.0 390.0 ; CAH NAD HAD 12 11 13 2 120.0<br>
>> 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<br>
>> O CA 5 4 6 7 2 0.0 167.4 0.0 167.4 ; imp<br>
>> N CA CAG CAH 7 5 8 11 2 0.0 167.4 0.0 167.4 ;<br>
>> imp CAH N NAE NAD 8 7 10 9 2 0.0 167.4 0.0<br>
>> 167.4 ; imp NAE CAH HAE HA6 11 7 13 12 2 0.0 167.4<br>
>> 0.0 167.4 ; imp NAD CAH HAD HA5 5 4 2 1 1 0.0<br>
>> 1.0 6 0.0 1.0 6 ; dih N CA C OXT 2 4 5 7 1<br>
>> 180.0 1.0 6 180.0 1.0 6 ; dih C CA N CAH 11 7 5<br>
>> 4 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD CAH N CA 5<br>
>> 7 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH NAE<br>
>> HAE 5 7 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih N<br>
>> 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<br>
>> 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<br>
>> 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>
>> 2010/11/15 Vitaly Chaban <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a> <mailto:<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>>><br>
>><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>
>><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>
> ========================================<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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<br>
Message: 3<br>
Date: Tue, 16 Nov 2010 20:03:03 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Protein in Electric Field<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4CE248C7.7020103@anu.edu.au">4CE248C7.7020103@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 16/11/2010 3:24 PM, S. Mohamadi wrote:<br>
> Dear All<br>
><br>
><br>
> I want to simulate a protein in Electric Field how can I do that?<br>
> where should I start from!<br>
> It's very Important for me! Please help me!<br>
><br>
> Thanks<br>
<br>
Start by looking in the manual.<br>
<br>
Mark<br>
<br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>--<br><br><font size="2"><b>With love and gratitude of,</b></font><br><br>Ithayaraja M,<br>Research Scholar,<br>Department of Bionformatics,<br>Bharathiar University,<br>
Coimbatore 641 046,<br>Tamil Nadu<br>India<br>