AMBER Archive (2006)

Subject: Re: AMBER: minimization of Hydrogens with xLeaP

From: David A. Case (
Date: Mon Nov 27 2006 - 20:19:48 CST

On Mon, Nov 27, 2006, wrote:

> I am a new user of AMBER and I have a problem with the minimization of the
> hydrogens of my protein. After introducing the hydrogens left in a PDB
> structure of a protein using xLeap, I tried to minimize these hydrogens fixing
> the rest of the atoms. For this, I used this input:
> &cntrl
> imin=1, maxcyc=5000, ncyc=250, ntb=0, igb=0, cut=10, ibelly=1,
> bellymask='@H=',
> /
> The energy of the minimization is stable, but the hydrogens appear very bad
> situated (the angles are not good). Does anybody know what I am doing wrong?

Maybe nothing. Why don't you try some regular (non-belly) minimization
as a comparison? Depending on how you obtained your initial coordinates (from
X-ray?) there may not be any acceptable geometries in which the heavy atoms
are completely identical to the initial coordinates. You still have large
forces in your calculation, which suggests that this may be the case.

...good luck...dac

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