Regard
Rituraj
On Fri, Jan 29, 2010 at 7:28 PM, <gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>> wrote:
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Today's Topics:
1. Re: Structure deformation (Carla Jamous)
2. Re: Structure deformation (Justin A. Lemkul)
3. Re: Re: including a custom itp file in topology (Tsjerk Wassenaar)
4. Re: RE: xmgrace (bharat gupta)
5. Re: RE: xmgrace (Justin A. Lemkul)
6. Re: RE: xmgrace (Baofu Qiao)
----------------------------------------------------------------------
Message: 1
Date: Fri, 29 Jan 2010 14:03:12 +0100
From: Carla Jamous <carlajam...@gmail.com
<mailto:carlajam...@gmail.com>>
Subject: Re: [gmx-users] Structure deformation
To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for
GROMACS users
<gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
Message-ID:
<e02c90f11001290503yce52eb7w45f7f23a53250...@mail.gmail.com
<mailto:e02c90f11001290503yce52eb7w45f7f23a53250...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"
Thank you Justin,
you were right I was looking at the wrong residue numbers.
I have another question that may also sound stupid, but I can't
figure it
out:
I want to extract from my trajectory, the protein, the ligand and ions.
However, when I try to do that with trjconv -f .trr -s .trr -n .ndx
gromacs asks to choose a group from my index file.
But if I choose group 0 1 2
it only takes the first group without the rest.
So how can I extract many groups at once from my trajectory?
Carla
On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
>
>
> Carla Jamous wrote:
>
>> Hi everyone,
>> I have a question about structure deformation
>> Can pdb2gmx alter secondary structures of my protein, while adding
>> hydrogens. Because I had a helix in my protein, that became a
beta-sheet
>> after pdb2gmx.
>>
>
> Sorry to say, but this sounds completely unlikely. A bug of this
magnitude
> surely would've been noticed long ago.
>
>
> What may be the problem?
>>
>>
> Are you certain you're looking at the same residues? pdb2gmx
renumbers
> from 1, so if there are missing N-terminal residues, they will
not have the
> same numbers before and after pdb2gmx.
>
> -Justin
>
> Thank you
>> Carla
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
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Message: 2
Date: Fri, 29 Jan 2010 08:04:11 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Structure deformation
To: "Gromacs Users' List" <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4b62dccb.8030...@vt.edu <mailto:4b62dccb.8030...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Carla Jamous wrote:
> Thank you Justin,
> you were right I was looking at the wrong residue numbers.
>
> I have another question that may also sound stupid, but I can't
figure
> it out:
> I want to extract from my trajectory, the protein, the ligand and
ions.
> However, when I try to do that with trjconv -f .trr -s .trr -n .ndx
> gromacs asks to choose a group from my index file.
> But if I choose group 0 1 2
> it only takes the first group without the rest.
> So how can I extract many groups at once from my trajectory?
Use make_ndx to merge the desired groups (i.e., 0 | 1 | 2) or simply !12
(assuming group 12 is SOL).
-Justin
>
> Carla
>
> On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>
>
>
> Carla Jamous wrote:
>
> Hi everyone,
> I have a question about structure deformation
> Can pdb2gmx alter secondary structures of my protein, while
> adding hydrogens. Because I had a helix in my protein, that
> became a beta-sheet after pdb2gmx.
>
>
> Sorry to say, but this sounds completely unlikely. A bug of this
> magnitude surely would've been noticed long ago.
>
>
> What may be the problem?
>
>
> Are you certain you're looking at the same residues? pdb2gmx
> renumbers from 1, so if there are missing N-terminal
residues, they
> will not have the same numbers before and after pdb2gmx.
>
> -Justin
>
> Thank you
> Carla
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
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> <mailto:gmx-users-requ...@gromacs.org
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>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 3
Date: Fri, 29 Jan 2010 14:07:25 +0100
From: Tsjerk Wassenaar <tsje...@gmail.com <mailto:tsje...@gmail.com>>
Subject: Re: [gmx-users] Re: including a custom itp file in topology
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID:
<8ff898151001290507q7cf83519s7dcac1d3aa8a9...@mail.gmail.com
<mailto:8ff898151001290507q7cf83519s7dcac1d3aa8a9...@mail.gmail.com>>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
rtp stands for 'Residue ToPology' and is used exclusively for building
block definitions, which are only used by pdb2gmx.
itp stands for 'Include ToPology' and can contain any part of a
topological description of a system, atom types, bond types,
moleculetypes, definitions, to be #included at the right point in the
master topology file. It is often used to separate out moleculetype
definitions, but also the top level force field parameters are
contained in a .itp file (ffoplsaa.itp for example).
For non standard residues, the residue has to be defined as a building
block and put in to a .rtp file in order to allow pdb2gmx to process
it. Non-bonded ligands need not be processed by pdb2gmx. With a proper
description in terms of coordinates and [ moleculetype ] (.itp file),
they can be easily merged with coordinates, c.q. topology as produced
by pdb2gmx.
Hope it helps,
Tsjerk
On Fri, Jan 29, 2010 at 1:45 PM, Jack Shultz
<j...@drugdiscoveryathome.com <mailto:j...@drugdiscoveryathome.com>> wrote:
> I confess I don't know the difference between rtp and itp. What I
was hoping
> was an easier way to generate topologies for complexes that have
> non-standard residue names like LIG. Alan's acpypi works.
You just have to
> do some extra scripting. But it seems like pdb2gmx should have a
way to load
> the files describing the non-standard residue names directly.
>
> On Fri, Jan 29, 2010 at 6:24 AM, Alan <alanwil...@gmail.com
<mailto:alanwil...@gmail.com>> wrote:
>>
>> Dear Berk,
>> I beg your pardon, but I have to assume that what you wrote
below is not
>> correct so, right?
>> Should it be 'ligand.rtp' instead of 'ligand.itp'?
>> Once I have my hands on this new pdb2gmx, I believe I can tweak
acpypi to
>> generate rtp files as well (but hdb and else probably not).
>> Cheers,
>> Alan
>>
>> On Fri, Jan 29, 2010 at 11:00, <gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>> wrote:
>>>
>>> > of them. So you can just put, e.g., a file called ligand.itp
in your
>>> > force
>>> > field or current dir and pdb2gmx
>>> > will read it.
>>
>>
>>
>> --
>> Alan Wilter Sousa da Silva, D.Sc.
>> PDBe group, PiMS project http://www.pims-lims.org/
>> EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge
CB10 1SD, UK
>> +44 (0)1223 492 583 (office)
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search
before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>
> --
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
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> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
------------------------------
Message: 4
Date: Fri, 29 Jan 2010 19:12:48 +0530
From: bharat gupta <bharat.85.m...@gmail.com
<mailto:bharat.85.m...@gmail.com>>
Subject: Re: [gmx-users] RE: xmgrace
To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for
GROMACS users
<gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
Message-ID:
<a15dd5271001290542m4ab253f1hea8d18193f9a2...@mail.gmail.com
<mailto:a15dd5271001290542m4ab253f1hea8d18193f9a2...@mail.gmail.com>>
Content-Type: text/plain; charset=ISO-8859-1
Thanks sir
But there is one problem that when I am running the mdrun step of 5th
step of lysozyme tutorial, I am getting an error :-
Can not open file:
topol.tpr
Can u tell me how to rectify it ..
------------------------------
Message: 5
Date: Fri, 29 Jan 2010 08:45:25 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] RE: xmgrace
To: "Gromacs Users' List" <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4b62e675.3010...@vt.edu <mailto:4b62e675.3010...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
bharat gupta wrote:
> Thanks sir
>
> But there is one problem that when I am running the mdrun step of 5th
> step of lysozyme tutorial, I am getting an error :-
>
> Can not open file:
> topol.tpr
>
> Can u tell me how to rectify it ..
>
No, since you haven't provided the command line you're using or what the
tutorial is expecting you to do.
If this is unrelated to your original post, please start a new
thread so the
archive doesn't get confusing.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 6
Date: Fri, 29 Jan 2010 14:56:24 +0100
From: Baofu Qiao <qia...@gmail.com <mailto:qia...@gmail.com>>
Subject: Re: [gmx-users] RE: xmgrace
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4b62e908.4030...@gmail.com
<mailto:4b62e908.4030...@gmail.com>>
Content-Type: text/plain; charset=ISO-8859-1
mdrun -s topol.tpr
BTW: take a look at "mdrun -h "
bharat gupta wrote:
> Thanks sir
>
> But there is one problem that when I am running the mdrun step of 5th
> step of lysozyme tutorial, I am getting an error :-
>
> Can not open file:
> topol.tpr
>
> Can u tell me how to rectify it ..
>
------------------------------
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