Hi.......
i have got some structures after ligand replacement and i have got energy
NaN in some of them.
and i have checked my structure through 'checkoverlap' command in
ptraj,there are some close
contacts between atoms,
since i have got these structure after ligand replacement so i can not
make change in structures,so is there any way to remove these close
contacts between atoms
what i have identified through 'checkoverlap' command .
plaese help me
pancham lal
IIT DELHI
On Tue, Oct 25, 2011 at 5:59 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 Wed Nov 02 2011 - 03:30:02 PDT
