Are your ligand residues sequential in the complex prmtop? If you ligand has
residues that are not sequential in the complex prmtop then the script will
not be able to guess the correct residue masks. If this is the case, then
add receptor_mask and ligand_mask in the &general section in mmpbsa.in with
the correct residues for each and try again. If your ligand is sequential in
your complex prmtop then you should double check the prmtops to make sure
they are consistent with one another.
Good luck!
-Bill
On Tue, May 25, 2010 at 6:15 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> I want to use MMPBSA and I gave the following command:
>
> $ MMPBSA.py -O -i mmpbsa.in -o results_mmpbsa.dat -sp 2o3me1c_wat.prmtop
> -cp
> 2o3me1c_vac.prmtop -rp 2o3m_vac.prmtop -lp lig_vac.prmtop -y
> 2o3me1c_md2.mdcrd
>
> It is showing the following:
>
> ptraj found! Using /root/amber11/bin/ptraj
> sander found! Using /root/amber9/exe/sander (serial only!)
> Assuming /root/amber9/exe/sander is part of
> amber9 or amber10. Using old PB input file.
> Error: Could not predict mask from topology files! Make sure ligand
> residues
> are
> sequential or specify receptor_mask and ligand_mask in the input file.
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
>
> (2o3me1c_wat.prmtop = prmtop of solvated complex
> 2o3me1c_vac.prmtop = prmtop of complex in vacuum
> 2o3m_vac.prmtop = prmtop of receptor in vacuum,
> lig_vac.prmtop = prmtop of ligand in vacuum,
> 2o3me1c_md2.mdcrd = mdcrd of final production run)
>
> Where am I going wrong?
>
> Kindly help,
> Asfa.
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 25 2010 - 04:00:03 PDT
