"If you have any custom-template residues this is often a
source of problems."
I have one custom made and when I look at the Gmax from the output file it
has a very high score. Furthermore, the residues around are displaced which
they are not supposed to do - I have included low vdw radii and the bonding
energy has a very high force constant (100 ) - can I get the clashing part
of Gmax out? When I look in the pdb it seems fine so there is a clash I am
not able to see.
On Thu, Jul 22, 2010 at 7:03 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > 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.
>
> Bill
>
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Received on Tue Jul 27 2010 - 12:00:03 PDT
