Hi,
Could you provide us with a little more detail: 1) are there any error
messages printed in the outputs files that you list in your previous email,
2) what is your input file and what version of AMBER are you using. Based
on the naming of your output files I am assuming you are using the perl
version MMPBSA. Do you get a similar error when you use MMPBSA.py (python
version), it is available in AmberTools13, which is free to download?
On Thu, Aug 1, 2013 at 10:29 PM, <nguyentb.bii.a-star.edu.sg> wrote:
> Dear AMBER users,
>
> After getting 2000 snapshot from the MD trajectory, I want to
> calculate both GPSA and PBSA for binding energy.
> However, one of the snapshots, after giving me snapshot_com.out within
> 1-2 minutes, it can't give full snapshot_rec.out up to 1-2 hours. The
> calculation stops at surface area calculation and gives
> snapshot_rec.pqr, snapshot_rec.pdb, snapshot_rec.mslog file.
>
> Could you please help me to solve this problem?
> Thanks in advance.
>
> Regards,
> Nguyen Thanh Binh
> PhD student, BII, Singapore
>
>
>
>
>
> _______________________________________________
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Thu Aug 01 2013 - 20:30:02 PDT
