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
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Received on Thu Aug 01 2013 - 14:30:03 PDT
