Re: [AMBER] How to use strip mask and receptor mask in the new mmpbsa.py?

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 22 Nov 2011 07:07:03 -0500

Try removing the : in front of the ..

However, ante-MMPBSA.py is fairly limited in its usefulness and applicability in this release. It generates an frcmod and OFF file from the main topology file and tries to create the topology files for the other systems via sleap.

The way it's implemented, it cannot recognize any dimer systems (anything with a charged amino acid terminus in the middle of the protein sequence), and it's dependent on how sleap creates topology files.

The next version will use a far more sophisticated approach that does not involve passing through leap -- it will modify the topology directly and only keep the parameters for the remaining atoms.

HTH,
Jason 

--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Nov 21, 2011, at 9:40 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Dear Amber users,
> I recently re-compiled AT15 and amber11, then realized the mmpbsa.py is upgraded. However, I cannot figure out how to use the receptor mask.  For example, in this command:
> ante-MMPBSA.py -p apt2loop13_solvated.prmtop -c apt2loop13_solvated.inpcrd -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -strip_mask ":WAT:Na+" -receptor_mask ":.1-5099"
> 
> 
> The receptor should include atoms 1 to 5099, but it didn't work.  What should be the right mask?  I am looking forward to your help.
> Thank you very much.
> 
> Best,
> Bin
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 22 2011 - 04:30:02 PST
Custom Search