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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Received on Wed Feb 10 2010 - 17:00:03 PST
