Okay fixed part of this error on my own.The reason is wasn't calculating the receptor or ligand was because I hadn't specified them correctly (or at all).
I assumed that since complex_prmtop was a default name (thus no need to specify it?), then receptor_prmtop, and ligand_prmtop would be too. My mistake. The speed thing I am looking into right now to get a comparison.
Best,
Jesper
________________________________________
From: Sorensen, Jesper [jesorensen.ucsd.edu]
Sent: Tuesday, June 18, 2013 7:12 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA.py and cpptraj error
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.
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?
I should say this is a fresh amber-installation as of yesterday with all updates and upgrades applied.
Jesper
On Jun 18, 2013, at 4:54 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Tue, Jun 18, 2013, Sorensen, Jesper wrote:
>
>> Warning: Box information present in parm but not in trajectory.
>
> This is the key: your prmtop file and trajectory files are not in sync
> with each other. If you have done any stripping, or otherwise changed
> to a non-periodic trajectory file, you need to create a prmtop file that
> matches the trajectory.
>
> ...dac
>
>
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Received on Tue Jun 18 2013 - 20:00:03 PDT
