Instructions for how to run mm_pbsa_statistics.pl can be found on a previous
thread posted by Dr. Gohlke (
http://structbio.vanderbilt.edu/archives/amber-archive/2006/0012.php).
Good luck!
-Bill Miller
On Mon, Mar 15, 2010 at 8:23 AM, Rama krishnan <ramki_rpcr.yahoo.com> wrote:
> Hi,
>
> the parameter file setting for mmpdsa is depends up on type of
> simulation. if u simulated using explicit water box, first strip all waters
> and ions if any from your trajectory. then generate prmtop file for all
> (say, protein, ligand and complex).. and edit the existing mmpbsa.in /
> snapshot.in file to run with mmpbsa.pl command (as per tutorial available
> in amber website). at last run free_energy.pl command fromt he same
> directory ( refer tutorial for file format
> http://ambermd.org/tutorials/advanced/tutorial3/ )....
>
> all the best
>
> with best regards
>
> C.Ramakrishnan.
> Scholar
> CAS in Crystallography and Biophysics
> University of Madras (Guindy Campus)
> Chennai - 600025
> Mobile : +91 98405 95180
>
>
> --- On Mon, 3/15/10, geyan <geyan.big.ac.cn> wrote:
>
> From: geyan <geyan.big.ac.cn>
> Subject: Re: Re: [AMBER] can't get the final "snapshot_statistics.out" file
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Monday, March 15, 2010, 2:05 PM
>
> first,thanks for your kind help.
> I have looked through the mm_pbsa_statistics.pl script. But I still
> don't konw how to set the exact parameters to get the final
> snapshot_statistics.out file if I have had the three out file.
> > snapshot_com.all.out
> > snapshot_rec.all.out
> > snapshot_lig.all.out
>
> so could you tell me how to set them?Thanks a lot.
> 2010-03-15
>
>
>
> geyan
>
>
>
> 发件人： Billy Miller III
> 发送时间： 2010-03-14 22:23:00
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: [AMBER] can't get the final "snapshot_statistics.out" file
>
> You should be able to use the mm_pbsa_statistics.pl script in
> $AMBERHOME/src/mm_pbsa/. This is the script that mm_pbsa.pl should be
> using
> to calculate the final snapshot_statistics.out file. This should work if
> there were no other problems with any of the other calculations.
> Good luck!
> -Bill Miller III
> 2010/3/13 geyan <geyan.big.ac.cn>
> > Dear all-amber users,
> > I need your help. When I performed the MM_PBSA analysis,everything
> seemed
> > OK before I got the final "snapshot_statistics.out" file. So can I
> calculate
> > by myself with the three separate following files?How to do?
> > snapshot_com.all.out
> > snapshot_rec.all.out
> > snapshot_lig.all.out
> >
> > Thank you for your kind help!Thanks a lot!
> >
> > 2010-03-14
> >
> >
> >
> > geyan
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> >
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Received on Mon Mar 15 2010 - 06:00:13 PDT
