Hello AMBER community,
I'm testing out MM-PBSA on a very small peptide (in this case just alanine
with ACE and NME caps).
I ran a kind of standard MM-PBSA using the following input file.
======
Sample input file with decomposition analysis
&general
startframe=1, endframe=50, interval=1, entropy=0, keep_files=0, verbose=1,
/
&gb
igb=5, saltcon=0.0, surften=0.0072,
/
&decomp
idecomp=2, dec_verbose=3,
print_res=2
/
======
Everything goes well and I get back some reasonable looking numbers. Then,
I tried switching entropy=0 to entropy=1 in order to get an entropy
estimate. I get this error:
======
Beginning quasi-harmonic calculation...
ERROR in tokenize(): wrong syntax
CalcError: /home/broom/Desktop/AMBER12/amber12/bin/ptraj failed with prmtop
ACE_ALA_NME.prmtop!
Exiting. All files have been retained.
========
I looked at the various temporary input files, and traced the problem to
the _MMPBSA_ptraj_entropy.in file:
========
trajin _MMPBSA_complex.mdcrd
reference _MMPBSA_avgcomplex.pdb
rms mass reference ,0-3
matrix mwcovar name comp.matrix ,0-3
analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce
========
When trying to run this alone through ptraj with my *.prmtop, I get the
same error as MMPBSA found. If I delete the ",0-3" portions, which I
believe represent a mask, the ptraj job completes. Of course, I don't know
if MMPBSA would work in that case because the run has already failed and I
have no sense of how to start things back up partway through.
It seems though that there is something wrong with either ptraj, or the way
MMPBSA is making its input files for this. I'm using ambertools12 and I
believe I'm fully uptodate on things, with ambertools patched to 28 and
amber to 13.
Has anyone else successfully run the entropy calculations with ambertools12
fully updated? One potential issue is that I don't really have receptors
and ligands, it's just a single trajectory of a single peptide that is
being considered a complex, but the non-entropy run completed without
trouble there, so I'm not sure that is the issue.
~Aron
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Nov 13 2012 - 14:00:04 PST
