[gmx-users] Plot renumbering
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 29 15:46:01 CET 2010
rituraj purohit wrote:
> 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 ?
Write a script that renumbers the file - perl, awk, sed, etc. I think pdb2gmx
renumbering is being removed in the development code for future versions, FYI.
-Justin
>
> Regard
> Rituraj
>
> On Fri, Jan 29, 2010 at 7:28 PM, <gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>> wrote:
>
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org <mailto:gmx-users-owner at gromacs.org>
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> 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
> <mailto:carlajamous at gmail.com>>
> Subject: Re: [gmx-users] Structure deformation
> To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
> GROMACS users
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <e02c90f11001290503yce52eb7w45f7f23a5325070d at mail.gmail.com
> <mailto: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
> <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
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100129/55ff7a64/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Fri, 29 Jan 2010 08:04:11 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] Structure deformation
> To: "Gromacs Users' List" <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4B62DCCB.8030703 at vt.edu <mailto: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>
> > <mailto: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> <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>
> > <mailto: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>
> > <mailto: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 <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 <tsjerkw at gmail.com <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <8ff898151001290507q7cf83519s7dcac1d3aa8a9ca9 at mail.gmail.com
> <mailto: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 <mailto: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
> <mailto: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
> <mailto: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
> <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
> >
> >
> >
> > --
> > Jack
> >
> > http://drugdiscoveryathome.com
> > http://hydrogenathome.org
> >
> > --
> > 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
> >
>
>
>
> --
> 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
> <mailto:bharat.85.monu at gmail.com>>
> Subject: Re: [gmx-users] RE: xmgrace
> To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
> GROMACS users
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <a15dd5271001290542m4ab253f1hea8d18193f9a2957 at mail.gmail.com
> <mailto: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 <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] RE: xmgrace
> To: "Gromacs Users' List" <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4B62E675.3010404 at vt.edu <mailto: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 <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 <qiaobf at gmail.com <mailto:qiaobf at gmail.com>>
> Subject: Re: [gmx-users] RE: xmgrace
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4B62E908.4030900 at gmail.com
> <mailto: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
> 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!
>
> End of gmx-users Digest, Vol 69, Issue 154
> ******************************************
>
>
>
>
> --
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list