Dear Dr. Jason
Yes, the problem was resturned to the mask term.
Thanks so much for your help
Sincerely;
S. Bill
--- On Thu, 11/2/10, Jason Swails <jason.swails.gmail.com> wrote:
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] MMPBSA.py error
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Thursday, 11 February, 2010, 0:57
Hello,
The masks do not appear correct. Those numbers should correspond to
residue numbers, not atom numbers (unless, of course, your system is
really composed of 3005 residues).
We are hoping to release a new version of the script soon that will
correctly guess the ligand_mask and receptor_mask simply by comparing
topology files, but until that happens, you'll have to correct these
two variables.
For this particular system, however, it looks like you may be able to
remove receptor_mask and ligand_mask from the input file altogether
anyway. The default guess in this version was that the ligand was
composed of a single residue and was the very last residue in the
complex topology file. If this is true, try removing those variables
and re-running the script.
Good luck!
Jason
On Wed, Feb 10, 2010 at 7:40 PM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBERI am so sorry for any inconvenience caused, but I found the problem is related to my ligand. pTraj has extracted the coordinates of the receptor without any problem, but it stopped at the ligand, I don't know why and hope you are able to help me.
> All the following files have been created:_MMPBSA_dummycomplex.inpcrd.1_MMPBSA_dummyreceptor.inpcrd.1_MMPBSA_cenptraj.in_MMPBSA_complexinpcrd.in_MMPBSA_ligandinpcrd.in
> _MMPBSA_ligtraj.in_MMPBSA_receptorinpcrd.in_MMPBSA_rectraj.inmmpbsa.in_MMPBSA_complex.mdcrd_MMPBSA_ligand.mdcrd_MMPBSA_receptor.mdcrd_MMPBSA_gb.mdin_MMPBSA_pb.mdin_MMPBSA_ptraj1.out_MMPBSA_ptraj2.out_MMPBSA_ptraj3.out_MMPBSA_ptraj4.out_MMPBSA_ptraj5.out_MMPBSA_ptraj6.out_MMPBSA_avgcomplex.pdb
>
> My mmpbsa.in was:Input file for running PB and GB in parallel&general solvated_prmtop='solvated_complex.prmtop',complex_prmtop="complex.prmtop", receptor_prmtop="receptor.prmtop", ligand_prmtop="ligand.prmtop", receptor_mask=:1-2996, ligand_mask=:2997-3005, endframe=250, verbose=1,/&gb igb=2, saltcon=0.000/&pb istrng=0.000, /
> I am so sorry again for disturbance.SincerelyS. Bill--- On Wed, 10/2/10, s. Bill <s_bill36.yahoo.co.uk> wrote:
>
> From: s. Bill <s_bill36.yahoo.co.uk>
> Subject: [AMBER] MMPBSA.py error
> To: "AMBER" <amber.ambermd.org>
> Date: Wednesday, 10 February, 2010, 23:46
>
> Dear AMBERI have a problem with running MMPBSA.py, and hope you could answer me.I have tested MMPBSA.py and it passed.During working on my system, I got this errorPreparing trajectories with ptraj... Error! Ptraj failed. Check coordinate and topology files for the complex.NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
> My system contains Zinc and Calcuim ions, should I modify something in MMPBSA.py script? Also, where should I add the bondi radii, as I did in mm_pbsa_calceneent.pm during using serial MM-PBSA?You should know that my system works well when I use the serail MM-PBSA.Thanks in advanceS. Bill
>
>
>
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Feb 11 2010 - 04:30:06 PST
