Hi Arvind,
When the hydrogens are added in leap, they are not placed at the energy
minimum. Some atoms might therefore be too close to other atoms in the
structure. A quick minimisation should fix it, either in xleap (edit
model->edit->relax) or in the minimisation step before running the MD
(ref. e.g. the DNA tutorial).
good luck,
Tormod
> It seems a lot of atoms are coming closer than they ought to be,
> physically. Why is these happening? I guess these would create problems
> later. Can somebody suggest me a way to get rid of these errors?
> Thanx in advance.
>
>
> Regards,
> Arvind.
>
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Received on Tue Apr 20 2004 - 16:53:00 PDT
