Re: [AMBER] minimization segmentation fault

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 22 Jul 2010 10:03:27 -0700

> The first of the minimization the energies explode which I presume are due
> to bad vdw interaction -clashing

The worst clashing atom is indicated by the GMAX part of the .out
file. If you have any custom-template residues this is often a
source of problems. Another possibility is the vdw-less H in
water, which depends on SHAKE to keep the H within the expanded
vdw of the O. I'm not sure what the defaults are, but ntc=2, ntf=2
will put SHAKE on H's.

Also you may be interested to know that low-temperature dynamics
will find a lower energy than minimization (10-100K) and will
sometimes get one out of a tight spot.


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Received on Thu Jul 22 2010 - 10:30:03 PDT
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