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 - 05:30:02 PDT
