I've succeeded in running ante-MMPBSA.py: it turns out I just needed to put quotes around my mask selections. From the solvated/ionized prmtop I created a complex (stripped water and ions) a receptor and a ligand prmtop file, however when running MMPBSA.py I get the following error:
"PrmtopError: provided receptor/ligand masks don't select every atom in the complex topology!
Exiting. All files have been retained."
I have selected every single residue in the protein for my receptor, and selected my ligand residue, so I do not see what the problem is. The only thing that I could think of is that the Na+ and Cl- ions in my original solvated prmtop might be causing problems. I will post my mmpbsa input script below if that helps:
Input file for running PB and GB
&general
startframe=85, endframe=200, verbose=1, interval=5, ligand_mask=:LIG, receptor_mask=:GLY,:TYR,:GLU,:VAL,:HIS,:GLN,:LYS,:LEU,:PHE,:ALA,:ASP,:SER,:ASN,:ILE,:MET
entropy=1,
/
&gb
ifqnt=1, qm_residues=:LIG,:GLY,:TYR,:GLU,:VAL,:HIS,:GLN,:LYS,:LEU,:PHE,:ALA,:ASP,:SER,:ASN,:ILE,:MET, qm_theory=AM1, qmcharge_com=-8, qmcharge_lig=4, qmcharge_rec=-12, igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
Thanks,
-Hunter
-----Original Message-----
>From: Jason Swails <jason.swails.gmail.com>
>Sent: Aug 1, 2013 12:14 PM
>To: Hunter Brown <bassoongoon.earthlink.net>, AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Using ante-mmpbsa.py to create prmtops
>
>On Thu, Aug 1, 2013 at 1:07 PM, Hunter Brown <bassoongoon.earthlink.net>wrote:
>
>> Hello, I am trying to create files for MMPBSA.py free energy analysis. My
>> complex topology file (stripped of water and ions) was created
>> successfully, however when ante-mmpbsa.py moved on to work on the receptor
>> (which I chose to be my protein structure) I got the following error. It
>> seems odd to me that the complex would have no problems, and then fail to
>> create the other files. I was just wondering what the problem might be? I
>> hope this is specific enough.
>>
>> Creating receptor topology file by stripping !(.8587-48269) from
>> 3foldposope2comp.prmtop
>>
>
>This seems like a strange ligand mask to be using. Your ligand is 40K
>atoms?
>
>Can you send me your prmtop and the ante-MMPBSA.py command you used?
>
>Also make sure you are using an up-to-date AmberTools 13 installation. [[
>$AMBERHOME/update_amber --version ]] should return AmberTools version
>13.14.
>
>All the best,
>Jason
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
Hunter Brown
Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
University of New Mexico
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 01 2013 - 14:30:02 PDT
