From: JIMENEZ Ralph (rjimenez_at_jilau1.Colorado.EDU)
Date: Tue Dec 06 2005 - 11:14:25 CST
I'm trying to minimize a system comprised of solvent, protein and
cofactor. I've been able to minimize solvent with fixed protein and
cofactor, followed by a second step in which everything is free to move.
I would like to minimize the system in three steps now. 1. solvent moves,
fixed protein and cofactor 2. solvent and protein moves, cofactor is
fixed. 3. solvent protein and cofactor all free to move.
I tried the following script, which failed. Each fixedAtomsFile specifies
a different set of fixed atoms.
# Minimization with fixed protein and heme first
# Minimization with fixed heme second
# now that solvent and peptide has been minimized, free the heme
When it fails, NAMD produces this error:
FATAL ERROR: Setting parameter fixedAtomsForces from script failed!
Apparently, it's not OK to reset fixedAtoms or fixedAtomsForces.
What's the right way to do it?
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