[gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

[Natalie Stephenson]

Yeah ... hadn't realised they were there when I began the simulating
Natalie
xxx
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 22 September 2010 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and     topology file not matching.

Natalie Stephenson wrote:
> Ok ... think I've worked out what's happened ...
> There were two 'SOL' groups.  So when replacing solvent with ions it has
> added double the amount of ions to the topol.top file.  Think I'll go
> back a couple of steps and try to sort out why there are two 'SOL' groups.

Were there water molecules (i.e., from a crystal structure) in the initial
structure passed to pdb2gmx?

-Justin

> Thanks for the help!
> xxx
>
>
> ------------------------------------------------------------------------
> *From:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Natalie Stephenson [Natalie.Stephenson at postgrad.manchester.ac.uk]
> *Sent:* 22 September 2010 13:02
> *To:* Discussion list for GROMACS users
> *Subject:* RE: [gmx-users] Energy minimisation problems - coordinate
> file and topology file not matching.
>
> Thanks for your help Justin & Terry
>
> I've been letting genion etc update it ... so there must be somewhere
> where i've missed it or something.  I'll check through the files and see
> if I can see what's missing...
>
> xxx
>
> ------------------------------------------------------------------------
> *From:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Terry [terrencesun at gmail.com]
> *Sent:* 22 September 2010 11:55
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Energy minimisation problems - coordinate
> file and topology file not matching.
>
>
> Hi, Natalie,
>
> Obviously, number of coordinates still doesn't match the topology file
> even you updated the topol.top *carefully*.
> Check the topol.top thoroughly or paste several line of your coordinate
> and topology files may be good ideas.
>
> Note that the topology file is lacking information for *28* atoms. Does
> that number remind you anything?
>
>
> Terry
>
> On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson
> <Natalie.Stephenson at postgrad.manchester.ac.uk
> <mailto:Natalie.Stephenson at postgrad.manchester.ac.uk>> wrote:
>
>     Hi everyone,
>
>     I was hoping you could clear up a problem I'm having when performing
>     energy minimisation.  I'm following the instructions from one of the
>     tutorials (Justin's Umbrella Sampling) with my own protein, however,
>     this time when I try to perform the energy minimisation it throws
>     out this 'fatal error message' ...
>
>      number of coordinates in coordinate file (nrr_solv_ions.gro, 33181)
>                  does not match topology (topol.top, 33153)
>
>     I've been updating the topol.top file every time I've done
>     something, so I'm not really sure what's happened.
>
>     Can anyone throw some light on what I've gone wrong!!
>     Thanks loads!
>     Natalie
>
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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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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