I did try it now with a DCD and it does work.
I assumed that it wouldn't based on reading the manual and running MMPBSA.py --help, which sort of specified that is "has" to be an mdcrd.
Best,
Jesper
On Jun 19, 2013, at 3:12 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 16:30:02 PDT
