Did you specify the receptor_mask and ligand_mask variables in your input
file? MMPBSA.py has a built in function to determine which residues
correspond to the receptor and which residues correspond to the ligand.
However, the guesser only works if all of the ligand residues are sequential
(one after the other with no receptor residues in between). If this is not
the case in your system, then you will need to specify receptor_mask and
ligand_mask in the &general section of the MMPBSA.py input file. Otherwise,
the guesser should work just fine, and if it isn't there might be an
inconsistency with the prmtops that you provided.
I hope that helps explain things a little better.
-Bill
On Tue, Jun 1, 2010 at 10:46 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> Dear Amber community members,
> Thanks Jason for a prompt help with the tutorial. I could use the new file
> successfully.
>
> I'm now trying the same tutorial procedure on my target protein and ligand.
> Here I'm getting a different kind of error which is given below. I could
> not
> understand what it exactly means and how could I fix it.
>
> Please find time and see if you could help me with same.
>
> The error is as follows:
> ---------------
> [vaibhav.localhost MMPBSA]$ $AMBERHOME/bin/MMPBSA.py -O -i
> mmpbsa_2b.inFINAL_RESULTS_MMPBSA.dat -sp 2PRG_rosi_solvated.prmtop -cp
> 2PRG_rosi_NW.prmtop -rp 2PRG_nolig.prmtop -lp rosi.prmtop -y *.mdcrd
> ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
> sander found! Using /home/vaibhav/software/amber10/exe/sander (serial
> only!)
> Assuming /home/vaibhav/software/amber10/exe/sander is part of
> amber9 or amber10. Using old PB input file.
> Error: Could not predict mask from topology files! Make sure ligand
> residues
> are
> sequential or specify receptor_mask and ligand_mask in the input file.
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
> [vaibhav.localhost MMPBSA]$ pwd
> /home/vaibhav/vaibhav/amber/2PRG/rosi/MMPBSA
> [vaibhav.localhost MMPBSA]$
> -------------------------------------------
>
>
> On 6/1/10, Jason Swails <jason.swails.gmail.com> wrote:
> >
> > Hello,
> >
> > On Tue, Jun 1, 2010 at 5:34 AM, vaibhav dixit <vaibhavadixit.gmail.com
> > >wrote:
> >
> >
> > > Dear Amber community members,
> > >
> > > I'm interested to calculate binding free energies for some of my
> ligands.
> > > In
> > > this regard I'm trying to use the following python script based
> tutorial
> > > http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
> > >
> > > After copying the Est_Rec_top_mdcrd.tgz and extracting it to get the
> > > necessary file, I ran the script using the command given in the
> tutorial.
> > > But I'm getting the following error and only two files are generated
> > > namely:
> > > _MMPBSA_gb.mdin and _MMPBSA_pb.mdin
> > >
> > > Please find time and see if you could help me in tracing the source of
> > the
> > > error.
> > >
> > > Thanking you all in anticipation and waiting for a reply...
> > >
> > > Error is given below
> > > -----------------------
> > > [vaibhav.localhost Estrogen_Raloxifene]$ $AMBERHOME/bin/MMPBSA.py -O
> -i
> > > mmpbsa_2b.in -o FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp
> > > complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
> > > ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
> > > sander found! Using /home/vaibhav/software/amber10/exe/sander (serial
> > > only!)
> > > Assuming /home/vaibhav/software/amber10/exe/sander is part of
> > > amber9 or amber10. Using old PB input file.
> > > Error: Could not find %FLAG POINTERS in topology file
> > 1err.solvated.prmtop!
> > >
> >
> >
> > Look at 1err.solvated.prmtop. %FLAG POINTERS is in every single prmtop
> > file
> > that I have ever seen (I daresay it must be present). This means that
> > 1err.solvated.prmtop is an invalid prmtop file. I just looked at it, and
> > it
> > appears corrupted for some reason (try to vi the file, it is a binary
> > file). I have placed 1err.solvated.prmtop on a separate location that
> you
> > can download and try:
> >
> > http://crunch.qtp.ufl.edu/~swails/Files/1err.solvated.prmtop<http://crunch.qtp.ufl.edu/%7Eswails/Files/1err.solvated.prmtop>
> >
> > Try downloading the file from there and using that one instead.
> >
> > Good luck!
> > Jason
> >
> >
> > NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> > > --clean to erase these files.
> > > ------------------------------------------------------
> > >
> > > --
> > > With regards
> > >
> > > Vaibhav A. Dixit
> > > Ph.D. Scholar
> > > Department of Medicinal Chemistry
> > > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > > Punjab -160 062 INDIA
> > > Phone (Mobile): +919915214408
> > > E-mail: vaibhavadixit.gmail.com
> > > www.niper.nic.in
> >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D. Scholar
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
> _______________________________________________
> AMBER mailing list
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 01 2010 - 08:00:06 PDT
