Hello,
I'm having issues performing an MMGBSA type calculation on a covalent
complex. The system has 413 residues, 1-412 being the protein, and 413
being the parameterized ligand. I have successfully performed a
simulation of several nanoseconds, and I'd like to find the effective
interaction energy of the protein against the ligand.
I've performed this with 4 other systems with this exact description,
using the exact input files, etc, but I have a different result for
this system. Here's the input:
&cntrl
ntb=0,
gbsa=2,
maxcyc=0,
ntc=1,
ntwx=1,
ntf=1,
idecomp=1,
cut=999.0,
irest=0,
imin=5,
ntmin=2,
igb=1,
/
Receptor
RRES 1 412
END
Ligand
LRES 413
END
Output
RES 1 413
END
END
There seems to be a post-processing-only issue with the ligand. I get
new warnings under the "Energy minimization:" section (though no
minimization is taking place):
Unusual nbond for C : 6354 1 Using default carbon
LCPO parameters
Unusual nbond for C : 6358 1 Using default carbon
LCPO parameters
Unusual nbond for C : 6370 1 Using default carbon
LCPO parameters
Unusual nbond for C : 6374 1 Using default carbon
LCPO parameters
Unusual nbond for C : 6440 1 Using default carbon
LCPO parameters
For reference, these carbon atoms are peripheral, on two valine-like
sidechains, and one at the end of a carbon chain. I've also deduced
that these lines:
Atom 6346 ( 413) : 0 3
should be displaying -413 instead of 0.
Finally, the complex and protein calculations, run separately, have
identical values, except for the addition of this line in the
complex's log:
TDC 413 0.000 0.000 0.000 0.000 0.000
This should usually give values other than 0, obviously. It seems that
the calculation is entirely ignoring my ligand in calculations.
Thanks to anyone with some insight on this issue.
--
Christopher C. Roberts
Department of Chemistry
University of California Riverside
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Received on Thu Oct 28 2010 - 15:00:02 PDT
