Again, I would suggest to use the latest release in Ambertool ... it's
better supported and maintained ...
All the best,
Ray
On Sat, Oct 22, 2011 at 10:46 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com> wrote:
> 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 Sun Oct 23 2011 - 08:30:02 PDT
