On Tue, Jun 18, 2013 at 10:12 PM, Sorensen, Jesper <jesorensen.ucsd.edu>wrote:
> I haven't exactly changed anything, but I did use ptraj (and cpptraj to
> test) to convert the trajectory from DCD to mdcrd, since MMPBSA.py won't
> accept dcd files.
>
Did you try this and get some error? MMPBSA.py should accept any
trajectory file that cpptraj can process. It passes the input trajectory
file immediately to cpptraj to generate the complex, receptor, and ligand
trajectory files.
> Now I went back and specified nobox in the ptraj step and this does get me
> past the cpptraj stage of the script.
>
> For the next stage as a test I am only using 1 frame, and here is my next
> problem.
> MMPBSA.py calculates this for the complex (very slowly compared to
> amber11), and then afterwards it stops and writes the FINAL....dat file,
> without having calculated the receptor or ligand contributions. Any clues
> here?
>
As you've already found out, specifying only the 'complex' topology file
indicates to MMPBSA.py that it should do a stability calculation. Since
only the complex topology file is required, only it has a 'default' value.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jun 19 2013 - 03:30:02 PDT
