AMBER Archive (2008)

Subject: AMBER: Running md using glycam in AMBER

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Thu Dec 11 2008 - 01:15:54 CST

Hi,

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.

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

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