On Fri, Sep 9, 2011 at 9:05 PM, Irene Newhouse <einew.hotmail.com> wrote:
>
>
>
>
> Ever since I compiled a parallel AMBER on my system, I've been having
> difficulties doing some of the standard file operations with tleap that
> worked when I only had a serial version. This is what happens: I start from
> a potein ligand complex. I manually edit the protein file from the complex,
> as well as the ligand file. I use commercial software to write a mol2 file
> from the ligand pdb file & antechamber to generate parameters. I then use
> tleap as follows:
>
> source leaprc.gaff
> loadAmberPrep flv.prepi
> lig = loadAmberParams flv.frcmod
> source leaprc.ff99SB
> pl = loadpdb cpd4spr.pdb
> p = loadpdb ns.pdb
> l = loadpdb cpd4s.pdb
> saveAmberParm l cpd4s.prmtop cpd4s.inpcrd
> saveAmberParm p ns.prmtop ns.inpcrd
> saveAmberParm pl cpd4sprnw.prmtop cpd4sprnw.inpcrd
> solvateBox pl TIP3PBOX 12.0
> addions pl Na+ 0
> addions pl Na+ 28 Cl- 28
> saveAmberParm pl cpd4spr.prmtop cpd4spr.inpcrd
>
> where pl designates the protein/ligand system, p the protein & l the ligand
> pdb file used to generate lig. I use NAMD to do the MD. I have no
> difficulty displaying the dcd file with VMD & manipulating it. Each of the
> various prmtop/inpcrd combinations are satisfactory for VMD. When I add the
> number of protein atoms as listed in the prmtop file to the number of ligand
> atoms listed in the ligand prmtop, the sum equals the number of atoms given
> in the complex prmtop. Yet, when I try to do MMGBSA, I get this error:
>
> Preparing 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.
>
Did you have a look at the _MMPBSA_ptraj*.out files? There should be some
error messages in that.
>
> The error message above was generated with
> receptor_mask=:1-201,ligand_mask=:202 in the namelist file for MMPBSA.py. I
> tried this because w/out it, the job failed as well, with this error:
>
> 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.
>
This arises due to the fact that MMPBSA.py can't reproduce the complex
residue sequence by combining the receptor and ligand residue sequences
(what it does is it tries to insert the ligand residues after each residue
in the receptor starting at the end, and it compares the sequences from the
combination with the complex sequence). What this error suggests is that
there is something funky about your topology files. Can you send them to me
to have a look at?
As a note, this should have nothing at all to do with the parallel version
of MMPBSA.
All the best,
Jason
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files. I looked at the retained files, & it appears
> that the MMPBSA.py crashes after generating a ligand mdcrd that it can't
> process.
> A couple of frames of the traj plus my prmtop files are way too big to send
> to everyone, although probably it will take having a look to debug them. If
> someone can help me, I can send the tarball directly. I'm bracing myself for
> ripping out the parallel installation & having to do MMPBSA serially & on
> far fewer points in future. Thanks!
> Irene Newhouse
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Sep 09 2011 - 20:30:02 PDT
