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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Natalie Stephenson [natalie.stephen...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Terry [terrence...@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.stephen...@postgrad.manchester.ac.uk
<mailto:natalie.stephen...@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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