AMBER Archive (2004)

Subject: Re: AMBER: nucgen generated RNA duplex: leap problems

From: Skauge Tormod (Tormod.Skauge_at_kj.uib.no)
Date: Tue Apr 20 2004 - 10:03:09 CDT

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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