On Tue, Oct 25, 2011, pancham lal gupta wrote:
>
> i have done ligand replacement,ligand may be small or large in comparison to
> first one.....
> when i have done energy minimisation,it gives energy NaN due to clashes of
> protein with ligand,
>
> How to remove clashes from structures? so that i can do energy
> minimisation.
We would need lots more information to be of much help. If you get an NaN on
the very first step, you need to look for why this is happening. The
"checkoverlap" command in ptraj can be a big help in identifying bad contacts.
Often, setting imin=1, and maxcyc=50, ncyc=50 (which forces steepest descent)
can help.
If you are getting NaN's after some number of steps, you may have a case where
a hydrogen (with no van der Waals radius) is getting too close to another atom.
This can happen if you don't have SHAKE turned on (set ntc=2). Again, you
*need* to find out what contact is causing the problem.
...dac
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Received on Tue Oct 25 2011 - 05:30:04 PDT
