Hi Amber users,
I wish to draw the attention of all Amber users and in particular the Amber
developers to a problem which I encountered while doing some entropy
calculations using nmode in amber 11.
I created prmtop files using the new ff99SBildn force field and used them as
input for mm_pbsa.pl and MMPBSA.py. The calculation stalls for MMPBSA.py
and gives an error that says that nmode is not working properly for
mm_pbsa.pl. I looked through the output files and found a line that said
"DIHEDRAL ANGLE ERROR". I searched through the amber archives and could not
find a satisfactory explanation for this error occurring. Finally I decided
to create my prmtop files using the ff99SB force field instead and the nmode
analysis could finally proceed. It took me almost 2 weeks to finally track
down what caused my nmode calculations to fail and the Amber forum was not
very useful, since I assume not many people are using the new force field
yet. I hope that the Amber developers will be able to work on a patch for
nmode so that we can use prmtop files created using the ff99SBildn force
field as input, just for the sake of consistency for those who run their
simulations using the new force field. I hope that this email will save
some people from the agony of troubleshooting their nmode analysis in
future. Thanks.
Regards,
Yaw Sing
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Received on Mon Feb 14 2011 - 10:30:05 PST
