AMBER: Questions on Phi, Psi angles produced by pmemd/sander7

From: Chen, Ya <>
Date: Sat, 23 Aug 2003 00:47:21 -0400

Hi, everyone,


I did a short run (<1ns) for a system of a small peptide in TIP3P water box using both pmemd and sander7 and found that the restart structures from equilibration (minimization followed by 75ps md) by pmemd and sander7 were quite different. The difference was maintained throughout production runs. Pmemd did not disrupt the molecule as much as sander7 when RMSDs are considered. But when examining individual residues, I found that for some residues, (Gly-Arg, in a beta-turn,) pmemd set disallowed (in Ramachandran plot) phi-psi values while phi-psi’s from sander7 are more allowed. By the end of the simulation, those disallowed phi-psi’s were not changed yet.

My questions:

Is it normal that some torsion angles are disallowed throughout simulation?

What is the possible cause of the inconsistency between pmemd and sander7 for my system?


The system was created with ff99 (Amber7) and temp=300 in production runs. The input files are identical. The starting structure (before minimization) was resolved from NMR spectra, without disallowed torsion angles.

Thanks for your help.



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Received on Sat Aug 23 2003 - 06:53:01 PDT
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