Thank you so much. I decided to let MMPBSA choose ligand and receptor masks.
Here is my modified input file:
Input file for running PB and GB
&general
startframe=85, endframe=200, verbose=1, interval=5,entropy=1,
/
&gb
ifqnt=1, qm_residues=:, qm_theory=AM1, qmcharge_com=-8, qmcharge_lig=4, qmcharge_rec=-12, igb=2, saltcon=0.100
/
&pb
istrng=0.100,
/
And here is the output (what is the selection error?):
Loading and checking parameter files for compatibility...
sander found! Using /home/Hunter/amber12/bin/sander
mmpbsa_py_energy found! Using /home/Hunter/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /home/Hunter/amber12/bin/cpptraj
ptraj found! Using /home/Hunter/amber12/bin/ptraj
SelectionError: Invalid selection! Integers expected.
Exiting. All files have been retained.
I appreciate the help,
-Hunter Brown
-----Original Message-----
>From: Jason Swails <jason.swails.gmail.com>
>Sent: Aug 1, 2013 3:16 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 5:05 PM, Hunter Brown <bassoongoon.earthlink.net>wrote:
>
>> 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
>>
>
>Do you mean to select all residues in qm_residues? If so, you can just use
>":*" instead.
>
>
>> /
>> &pb
>> istrng=0.100,
>> /
>>
>
>Your ligand_mask and receptor_mask seems like overkill to me. And based on
>the error message you're getting, it appears that your mask selection is
>not selecting everything. The default mask guesser should be able to
>accommodate your system (and will print out an error if it cannot).
>
>You should check that Na+ and Cl- are not present in your receptor and
>ligand topology files using the "printDetails" command in ParmEd. You can
>actually use ParmEd to check all of your masks. For instance, the output
>from
>
>printDetails !(:GLY,:TYR,:GLU,:VAL,:HIS,:GLN,:LYS,:LEU,:PHE,:
>ALA,:ASP,:SER,:ASN,:ILE,:MET)
>
>should return _just_ the residues in LIG if that mask is correct. (and [[
>printDetails :Na+,Cl- ]] will tell you if you forgot to have ante-MMPBSA.py
>remove the ions).
>
>At the end of the day, letting MMPBSA.py guess its own masks is often the
>safest route, since it adds a layer of error checking for most systems.
>
>HTH,
>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
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Received on Fri Aug 02 2013 - 10:30:22 PDT
