[gmx-users] query about protein-ligand complex

[Tsjerk Wassenaar]

Hi Sangeeta,

Also check whether you have isolated water molecules in your system
(notably the one starting at atom id 13339). If so, that may be a
cause of crash and it would be better just to delete the water
molecule.

Best,

Tsjerk

On 7/3/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> sangeeta wrote:
> > I could not mail you as our net was down,
> > you asked me "Is your system
> >  properly minimized? "
> > My question is how can I understand whether my system is properly minimised?
>
> Look at the structure before you minimize it, and look at the structure
> after you minimize it. See what has changed and use some chemical
> judgement. If you're uncertain of yourself, experiment with some smaller
> systems before using a system as large as yours.
>
> Mark
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336