[gmx-users] Orders of the residues in gromacs

[Joaquim Rui de Castro Rodrigues]

Hi,

You are probably mixing "resid" and "residue". In VMD, 
 - "resid" is taken as found in the file (pdb, gro, etc). You may have several residues with the same "resid" if you load a file with multiple chains.
 - "residue" is generated internally by VMD, it is incremented by one unit for each residue, even if there are gaps in the sequence, it always starts at 0 and is granted to be unique for each residue.

Cheers,
Rui Rodrigues



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De: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] Em Nome De Du Jiangfeng (BIOCH) [j.du at maastrichtuniversity.nl]
Enviado: sexta-feira, 3 de Fevereiro de 2012 9:06
Para: gmx-users at gromacs.org
Assunto: [gmx-users] RE: gmx-users Digest, Vol 94, Issue 24

Dear All,

I found a strange thing about VMD. When I use mouse label residue from graph (Mouse --> Label --> Atom), i would get a correct residue as it is in .gro file, while when I use graphics --> representations --> selections, then the residue selected here is totally different with the one which has the same number in the .gro file.

Be careful with it, everybody.
Jiangfeng.

    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands
________________________________________



Dear Friends,

I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem.

The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file.

Does anybody know how to link the gromacs order to the structure file's order correctly?

Thank you in advance,

Jiangfeng.



    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands

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Message: 4
Date: Thu, 02 Feb 2012 12:43:17 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2ACB35.8050808 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Du Jiangfeng (BIOCH) wrote:
> Dear Friends,
>
> I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem.
>
> The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file.
>
> Does anybody know how to link the gromacs order to the structure file's order correctly?
>

Depending on the Gromacs version you're using, residue numbering is treated
differently.  In pdb2gmx, you can choose to renumber the residues from 1 or not.
  The default is to not renumber the file.  You should check to see what you did
with respect to this option and whether or not your coordinate file is numbered
from 1.  If it is not, then what you think is residue 143 may not be interpreted
that way by all external programs, depending on whether or not they respect the
numbering of the .gro file.

-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

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Message: 8
Date: Fri, 3 Feb 2012 10:04:28 +0800 (SGT)
From: Jianguo Li <ljggmx at yahoo.com.sg>
Subject: Re: [gmx-users] Orders of the residues in gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <1328234668.1600.YahooMailNeo at web190204.mail.sg3.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Another possible reason is due to vmd, which numbers the residue from 0. Residue 143 in gromacs corresponds to residue 142 in vmd.
Cheers,

Jianguo



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