[gmx-users] Plot renumbering
rituraj purohit
riturajpurohit at gmail.com
Fri Jan 29 15:40:36 CET 2010
Hello friends,
As Justin replied at carla query about structure deformation after the
pdb2gmx & the new number retain till end.
My PDB starts at 24 to 200 aa, While running xmgrace (after complete
simulation) the rmsd plot is from 1 to 176aa.
I understood by previous mail that gromacs renumbered my pdb file at first
step.
My question is, Is their any way to get plot from 24 to 200 (as entry in
pdb) rather 1 to 174 ?
Regard
Rituraj
On Fri, Jan 29, 2010 at 7:28 PM, <gmx-users-request at 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 <carlajamous at gmail.com>
> Subject: Re: [gmx-users] Structure deformation
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <e02c90f11001290503yce52eb7w45f7f23a5325070d at 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 <jalemkul at 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 | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at 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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> ------------------------------
>
> Message: 2
> Date: Fri, 29 Jan 2010 08:04:11 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Structure deformation
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4B62DCCB.8030703 at 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 <jalemkul at vt.edu
> > <mailto:jalemkul at 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 at gromacs.org
> > <mailto:gmx-users at 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-request at gromacs.org
> > <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]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 <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Re: including a custom itp file in topology
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <8ff898151001290507q7cf83519s7dcac1d3aa8a9ca9 at 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 <js at 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 <alanwilter at 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-request at 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 at 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-request at 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 at 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-request at 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.monu at gmail.com>
> Subject: Re: [gmx-users] RE: xmgrace
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <a15dd5271001290542m4ab253f1hea8d18193f9a2957 at 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] RE: xmgrace
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4B62E675.3010404 at 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 | (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 <qiaobf at gmail.com>
> Subject: Re: [gmx-users] RE: xmgrace
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B62E908.4030900 at 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 ..
> >
>
>
>
> ------------------------------
>
> --
> gmx-users mailing list
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 69, Issue 154
> ******************************************
>
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