Dear Ray,
Yes, I would definitely go for AMBERTOOLS1.5 !
Thanks for your reply!
Qiong
On Sun, Oct 23, 2011 at 5:23 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
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Received on Sun Oct 23 2011 - 08:30:03 PDT
