On Thu, Oct 24, 2013 at 8:31 AM, Indrajit Deb <biky2004indra.gmail.com>wrote:
> Dear AMBER users
>
> I am a beginner of AMBER trying to run MMPBSA.py on a set of PDB of a
> Protein-DNA complex, which is extracted form a trajectory file. Like single
> trajectory method I have generated receptor and ligand pdbs from the
> respective complex pdb. Respective prmtop and inpcrd files were generated
> using AMBER12 and used for MMPBSA.py as
>
>
> MMPBSA.py -O -i mmpbsa.in -o RESULTS_MMPBSA$counter0b.dat -do
> FINAL_DECOMP_MMPBSA$counter0b.dat -cp comp_mod$counter0b.prmtop -rp
> Protein_mod$counter0b.prmtop -lp DNA_mod$counter0b.prmtop -y
> comp_mod$counter0b.inpcrd
>
> where $counter0b is a variable.
>
> My questions are:
> 1. Whether the method is logical or not?
>
I have no idea, you didn't actually describe a method. You gave a
command-line that you used that might be valid (assuming counter0b is a
recognized shell variable, the necessary input files exist, and you have
write permissions on the file system you are running on) or might not.
> 2. MMPBSA.py giving error if I used 99SBildn or 99bsc0 but work fine for
> 99SB.
>
This is probably an error typing issue. Make sure you are using the latest
version of AmberTools 13 with all updates applied. The configure part of
the build process should handle the updates (just make sure you actually
compile Amber after the updates have been applied).
> 3. per residue decomposition gives following error:
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd.1" is missing or
> unreadable
>
I can't reproduce this issue with the current version of MMPBSA.py. The
only time I've seen this problem was with a single-frame trajectory in
AmberTools 12 before bugfix.9 was applied. If this is the problem,
updating as I suggested above will fix it. If not, I need more context of
the error to help (and I may need to reproduce the error myself).
In general, when you ask for help you need to give detailed information.
Give us exact commands and exact output (after making sure you've applied
all bug fixes and updates), and/or any information we would need to run the
calculation ourselves to reproduce the problem.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 24 2013 - 07:30:03 PDT
