Dear all Amber users,
I had a problem with mm_pbsa analyses for the binding free energy with PBSA
module in amber 11. The script I used is the perl script named mm_pbsa.pl.
When PB is used (PB=1), I got the similar error as this:
http://archive.ambermd.org/201107/0580.html, Attached are my input file for
this mm_pbsa analysis (binding_energy.mmpbsa) and the log file
(binding_energy.log). *It has produced the output
files:snapshot_com.all.out,snapshot_rec.all.out,snapshot_lig.all.out,but not
"snapshot_statistics.out ".
*
But I tried the test example under the $AMBERHOME/src/mm_pbsa/Example
directory for the binding free energy calculation where PB is used, it works
fine.
Then I tried mm_pbsa_statistics.pl to do statistics from the three
files *snapshot_com.all.out,snapshot_rec.all.out,snapshot_lig.all.out,
*It does not work either. Attached is the error message for the statistics
(statis.log). "WARNING: Missing SURF for MS ...."
I noticed* the difference between my input file for mm_pbsa and that in the
test example is that I did not turn on MS calculation for the nonpolar
contribution to the solvation free energy (MS=0).*
However, as far as I understand, and also stated in the manual, # If MS ==
0 and PB == 1, nonpolar contributions are calculated according the INP
option in pbsa. That's why I have turned off MS. And For the NP Parameters
for nonpolar solvation energies if MS = 0, I had the following setup:
RADIOPT 1
INP 2
*Sofar, it seems to me that for this perl script, when PB=1, no matter MS is
turned off or not, the nonpolar contribution would still be calculated by MS
(molsur) approach. So when I turned off MS, it would give this error message
"WARNING: Missing SURF for MS ...." .* *Is this true??
*
I have confirmed this issue for my case by turning on MS (PB=1, MS=1) in the
analysis, now PB calculation also works fine. *So this should be a bug??*
It* works fine when GB=1, MS=0*, since nonpolar contributions are calculated
with the LCPO method in sander.
As suggested by Prof. Ray Luo, for mm_pbsa analyses, now we'd better use
AMBERTOOLS with better controled parameters. I think with the newest release
AMBERTOOLS1.5, this won't be a issue any more. I will try that!
Any comments or suggestions would be greatly appreciated!
Kind regards,
Qiong
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Received on Sat Oct 22 2011 - 23:00:04 PDT
