AMBER: RE: gaff sugar residue instability

From: hayden <>
Date: Tue, 22 Nov 2005 19:32:14 -0000

Dear amber users


I have recently created a phosphorylated sugar residue using gaussian and
resp procedures. The molecule was successfully created and made into a prep
file. I checked this molecule within leap and it gave no error readings once
I had specified all the connect atoms.


I have run dynamics on the molecule beginning at 0 K with high coupling to
the heat bath (ntt=1) and gradually relaxed the restraints on the molecule
over time. Once it was producing steady dynamics I removed the restraints
and performed ordinary dynamics at 300K for 300 picoseconds. I then took
this structure and minimized it to produce my final structure. However, the
problem is that if I run dynamics on this minimized construct at higher
temperatures (say 350 K) I get blow outs. Therefore my questions are:


1. Does my construct require further equilibration? (surely not - I;ve
done approximately 3 nanoseconds.)
2. If not, is there something more severely wrong with my molecule?
Perhaps an error in the gaff parameters for certain connectivities within my
construct? I've made other sugars that do not suffer from this problem.
3. Are saccharide moieties like this more prone to blow outs than


Many thanks in advance





Hayden Eastwood

Perdita Barran Research Group

Joseph Black Building

Edinburgh University

West Mains Road



Tel: 0131 650 4773


Research page:

"You have to be an academic to believe some things; no ordinary person would
be so stupid." -George Orwell


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Received on Tue Nov 22 2005 - 19:53:01 PST
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