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

[Natalie Stephenson]

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.
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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