Thanks, Charles. Changing test to [test] worked.
Now the problem is that the secondary structure is perturbed. The
backbone RMSD between input and output structures is 1.1 Angstroms. I
called in the input structure in the create_PosDiffPot for the
comparison. Will adding pdbFile to create_PosDiffPot enforce the new
structure to adopt the same backbone atom positions?
####################################
try:
protocol.addUnknownAtoms(dyn_stepsize=0.01)
test=create_PosDiffPot("test",selection="(name CA or name C or
name N or name O) and resid 64:184",
pdbFile='apoIsdA_metchanged2.pdb')
minimizeRefine([test],
refineSteps=50,
xplorPots=['BOND','ANGL','IMPR','VDW','RAMA'])
#fix geom everything but modified sites
protocol.fixupCovalentGeom(sel=fixGeom,verbose=2,useVDW=1,maxIters=10)
open(successFile,"w").write("ok")
except protocol.CovalentViolation:
pass
######################################
Thanks,
Valerie
On Tue, Sep 29, 2009 at 7:39 AM, <Charles at schwieters.org> wrote:
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> Hello Valerie--
>
>> I tried using posDiffPot and simulationTools.minimizeRefine to
>> regularize the atomic positions after adding CYSP-MTSL and protons to
>> a crystal structure:
>
> try changing your minimizeRefine call to
>
> minimizeRefine([test],
> ? ? ? ? ? ? ? refineSteps=50,
> ? ? ? ? ? ? ? xplorPots=['BOND','ANGL','IMPR'])
>
>
> best regards--
> Charles
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