AMBER Archive (2008)

Subject: RE: AMBER: Running md using glycam in AMBER

From: Matthew Tessier (
Date: Thu Dec 11 2008 - 14:52:28 CST


I'm very interested in this because we've been trying to optimize the
GLYCAM06 force field to better reproduce transitional ring structures like
Idose and Iduronic acid which are typically found in a mixture of non-4C1
conformations. Our preliminary work has indicated that the charge set
greatly impacts the transitions and lifetimes of mixed-state sugars. I
can't speak to your coupling parameters, but I would be very interested to
hear about your Iduronic acid simulations. Please contact me off-list to
discuss your results.


Matthew Tessier

Woods' Lab Room 1092

Complex Carbohydrate Research Center - University of Georgia


From: [] On Behalf Of
Neha Gandhi
Sent: Thursday, December 11, 2008 2:16 AM
To:; CCL Subscribers;
Subject: AMBER: Running md using glycam in AMBER



I am trying to reproduce Cremer-pople parameters for iduronic acid. I am
using glycam biomolecular builder to prepare input files ie. pdb,
coordinates and topology files for alpha-L-IdoA-OH. The same tool assigns
TIP3P and metal ions to neutralize the charge. I followed energy
minimization followed by heating and NPT for 500 ps equlibriation. NPT was
used to parameterize Glycam06 forcefields and I am using the same protocol.
But during MD very frequent conformational transitions are observed for
iduronic acid starting from 1C4 conformation. I expected that for the first
100 or 200 ps theta angle angle would be around 180 degrees followed by a
transition to 2S0 but my results are random.

Could anybody help me if the coupling parameters for heat bath (0.1, 0.25,1
or 2) and pressure coupling (0.5 to 2) will change this conformational
equlibria? It would be great if somebody can provide the sander mdin files
to validate the parameters.

Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

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