From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Tue Dec 06 2005 - 12:31:36 CST
why don't you try to do one thing at a time using 3 different config
files for namd?
Marc
On Dec 6, 2005, at 12:14 PM, JIMENEZ Ralph wrote:
> Hi everyone:
> 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
> fixedAtoms yes
> fixedAtomsForces yes
> fixedAtomsFile /data1/rjimenez/FixLsim/oxy/oxyFixLsolv_neut.pdb
> fixedAtomsCol B
> minimize 10000
> # Minimization with fixed heme second
> fixedAtoms yes
> fixedAtomsForces yes
> fixedAtomsFile /data1/rjimenez/FixLsim/oxy/oxyFixLsolv_neutHemeFix.pdb
> fixedAtomsCol B
> minimize 10000
> # now that solvent and peptide has been minimized, free the heme
> fixedAtoms no
> minimize 10000
>
> 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?
>
> Thanks,
> Ralph
>
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