Hello friends,<br><br>As Justin replied at carla query about structure deformation after the pdb2gmx & the new number retain till end.<br><br>My PDB starts at 24 to 200 aa, While running xmgrace (after complete simulation) the rmsd plot is from 1 to 176aa.<br>
<br>I understood by previous mail that gromacs renumbered my pdb file at first step.<br>My question is, Is their any way to get plot from 24 to 200 (as entry in pdb) rather 1 to 174 ?<br><br>Regard<br>Rituraj<br><br><div class="gmail_quote">
On Fri, Jan 29, 2010 at 7:28 PM, <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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: Structure deformation (Carla Jamous)<br>
2. Re: Structure deformation (Justin A. Lemkul)<br>
3. Re: Re: including a custom itp file in topology (Tsjerk Wassenaar)<br>
4. Re: RE: xmgrace (bharat gupta)<br>
5. Re: RE: xmgrace (Justin A. Lemkul)<br>
6. Re: RE: xmgrace (Baofu Qiao)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 29 Jan 2010 14:03:12 +0100<br>
From: Carla Jamous <<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>><br>
Subject: Re: [gmx-users] Structure deformation<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:e02c90f11001290503yce52eb7w45f7f23a5325070d@mail.gmail.com">e02c90f11001290503yce52eb7w45f7f23a5325070d@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thank you Justin,<br>
you were right I was looking at the wrong residue numbers.<br>
<br>
I have another question that may also sound stupid, but I can't figure it<br>
out:<br>
I want to extract from my trajectory, the protein, the ligand and ions.<br>
However, when I try to do that with trjconv -f .trr -s .trr -n .ndx<br>
gromacs asks to choose a group from my index file.<br>
But if I choose group 0 1 2<br>
it only takes the first group without the rest.<br>
So how can I extract many groups at once from my trajectory?<br>
<br>
Carla<br>
<br>
On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<br>
><br>
><br>
> Carla Jamous wrote:<br>
><br>
>> Hi everyone,<br>
>> I have a question about structure deformation<br>
>> Can pdb2gmx alter secondary structures of my protein, while adding<br>
>> hydrogens. Because I had a helix in my protein, that became a beta-sheet<br>
>> after pdb2gmx.<br>
>><br>
><br>
> Sorry to say, but this sounds completely unlikely. A bug of this magnitude<br>
> surely would've been noticed long ago.<br>
><br>
><br>
> What may be the problem?<br>
>><br>
>><br>
> Are you certain you're looking at the same residues? pdb2gmx renumbers<br>
> from 1, so if there are missing N-terminal residues, they will not have the<br>
> same numbers before and after pdb2gmx.<br>
><br>
> -Justin<br>
><br>
> Thank you<br>
>> Carla<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>
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------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 29 Jan 2010 08:04:11 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Structure deformation<br>
To: "Gromacs Users' List" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4B62DCCB.8030703@vt.edu">4B62DCCB.8030703@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Carla Jamous wrote:<br>
> Thank you Justin,<br>
> you were right I was looking at the wrong residue numbers.<br>
><br>
> I have another question that may also sound stupid, but I can't figure<br>
> it out:<br>
> I want to extract from my trajectory, the protein, the ligand and ions.<br>
> However, when I try to do that with trjconv -f .trr -s .trr -n .ndx<br>
> gromacs asks to choose a group from my index file.<br>
> But if I choose group 0 1 2<br>
> it only takes the first group without the rest.<br>
> So how can I extract many groups at once from my trajectory?<br>
<br>
Use make_ndx to merge the desired groups (i.e., 0 | 1 | 2) or simply !12<br>
(assuming group 12 is SOL).<br>
<br>
-Justin<br>
<br>
><br>
> Carla<br>
><br>
> On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>
><br>
><br>
><br>
> Carla Jamous wrote:<br>
><br>
> Hi everyone,<br>
> I have a question about structure deformation<br>
> Can pdb2gmx alter secondary structures of my protein, while<br>
> adding hydrogens. Because I had a helix in my protein, that<br>
> became a beta-sheet after pdb2gmx.<br>
><br>
><br>
> Sorry to say, but this sounds completely unlikely. A bug of this<br>
> magnitude surely would've been noticed long ago.<br>
><br>
><br>
> What may be the problem?<br>
><br>
><br>
> Are you certain you're looking at the same residues? pdb2gmx<br>
> renumbers from 1, so if there are missing N-terminal residues, they<br>
> will not have the same numbers before and after pdb2gmx.<br>
><br>
> -Justin<br>
><br>
> Thank you<br>
> Carla<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> <<a href="http://vt.edu" target="_blank">http://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>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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><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>
------------------------------<br>
<br>
Message: 3<br>
Date: Fri, 29 Jan 2010 14:07:25 +0100<br>
From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
Subject: Re: [gmx-users] Re: including a custom itp file in topology<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:8ff898151001290507q7cf83519s7dcac1d3aa8a9ca9@mail.gmail.com">8ff898151001290507q7cf83519s7dcac1d3aa8a9ca9@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hi,<br>
<br>
rtp stands for 'Residue ToPology' and is used exclusively for building<br>
block definitions, which are only used by pdb2gmx.<br>
itp stands for 'Include ToPology' and can contain any part of a<br>
topological description of a system, atom types, bond types,<br>
moleculetypes, definitions, to be #included at the right point in the<br>
master topology file. It is often used to separate out moleculetype<br>
definitions, but also the top level force field parameters are<br>
contained in a .itp file (ffoplsaa.itp for example).<br>
<br>
For non standard residues, the residue has to be defined as a building<br>
block and put in to a .rtp file in order to allow pdb2gmx to process<br>
it. Non-bonded ligands need not be processed by pdb2gmx. With a proper<br>
description in terms of coordinates and [ moleculetype ] (.itp file),<br>
they can be easily merged with coordinates, c.q. topology as produced<br>
by pdb2gmx.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
On Fri, Jan 29, 2010 at 1:45 PM, Jack Shultz <<a href="mailto:js@drugdiscoveryathome.com">js@drugdiscoveryathome.com</a>> wrote:<br>
> I confess I don't know the difference between rtp and itp. What I was hoping<br>
> was an easier way to generate topologies for complexes that have<br>
> non-standard residue names like LIG. Alan's acpypi works. You just have to<br>
> do some extra scripting. But it seems like pdb2gmx should have a way to load<br>
> the files describing the non-standard residue names directly.<br>
><br>
> On Fri, Jan 29, 2010 at 6:24 AM, Alan <<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>> wrote:<br>
>><br>
>> Dear Berk,<br>
>> I beg your pardon, but I have to assume that what you wrote below is not<br>
>> correct so, right?<br>
>> Should it be 'ligand.rtp' instead of 'ligand.itp'?<br>
>> Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to<br>
>> generate rtp files as well (but hdb and else probably not).<br>
>> Cheers,<br>
>> Alan<br>
>><br>
>> On Fri, Jan 29, 2010 at 11:00, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br>
>>><br>
>>> > of them. So you can just put, e.g., a file called ligand.itp in your<br>
>>> > force<br>
>>> > field or current dir and pdb2gmx<br>
>>> > will read it.<br>
>><br>
>><br>
>><br>
>> --<br>
>> Alan Wilter Sousa da Silva, D.Sc.<br>
>> PDBe group, PiMS project <a href="http://www.pims-lims.org/" target="_blank">http://www.pims-lims.org/</a><br>
>> EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK<br>
>> +44 (0)1223 492 583 (office)<br>
>><br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the<br>
>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
><br>
><br>
> --<br>
> Jack<br>
><br>
> <a href="http://drugdiscoveryathome.com" target="_blank">http://drugdiscoveryathome.com</a><br>
> <a href="http://hydrogenathome.org" target="_blank">http://hydrogenathome.org</a><br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 29 Jan 2010 19:12:48 +0530<br>
From: bharat gupta <<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>><br>
Subject: Re: [gmx-users] RE: xmgrace<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:a15dd5271001290542m4ab253f1hea8d18193f9a2957@mail.gmail.com">a15dd5271001290542m4ab253f1hea8d18193f9a2957@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Thanks sir<br>
<br>
But there is one problem that when I am running the mdrun step of 5th<br>
step of lysozyme tutorial, I am getting an error :-<br>
<br>
Can not open file:<br>
topol.tpr<br>
<br>
Can u tell me how to rectify it ..<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Fri, 29 Jan 2010 08:45:25 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] RE: xmgrace<br>
To: "Gromacs Users' List" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4B62E675.3010404@vt.edu">4B62E675.3010404@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
bharat gupta wrote:<br>
> Thanks sir<br>
><br>
> But there is one problem that when I am running the mdrun step of 5th<br>
> step of lysozyme tutorial, I am getting an error :-<br>
><br>
> Can not open file:<br>
> topol.tpr<br>
><br>
> Can u tell me how to rectify it ..<br>
><br>
<br>
No, since you haven't provided the command line you're using or what the<br>
tutorial is expecting you to do.<br>
<br>
If this is unrelated to your original post, please start a new thread so the<br>
archive doesn't get confusing.<br>
<br>
-Justin<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>
------------------------------<br>
<br>
Message: 6<br>
Date: Fri, 29 Jan 2010 14:56:24 +0100<br>
From: Baofu Qiao <<a href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</a>><br>
Subject: Re: [gmx-users] RE: xmgrace<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:4B62E908.4030900@gmail.com">4B62E908.4030900@gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
<br>
mdrun -s topol.tpr<br>
<br>
BTW: take a look at "mdrun -h "<br>
<br>
bharat gupta wrote:<br>
> Thanks sir<br>
><br>
> But there is one problem that when I am running the mdrun step of 5th<br>
> step of lysozyme tutorial, I am getting an error :-<br>
><br>
> Can not open file:<br>
> topol.tpr<br>
><br>
> Can u tell me how to rectify it ..<br>
><br>
<br>
<br>
<br>
------------------------------<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>