On Tue, Jun 11, 2013 at 5:09 AM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Dear AMBER user,
>
> I think I have exactly the same problem with this post. I used Amber 11,
> and mmpbsa.pl script to calculate the binding free energy for a
> protein-ligand complex.
>
> It actually did not show any specific error in the log file, but the
> calculation just terminated (at com.6).
> According to the archive posts, the problem may be the memory -involved.
> Do you have any idea how to overcome it? Please help.
>
It doesn't sound like a memory-related issue.
> .Jason Swails: will the mmpbsa.py solve the memory problem? I am using
> AmberTools1.5, and as you suggested to some friend in the AMBER list to use
> mmpbsa.py (AmberTools13), can I ask a trivial question (sorry I am one of
> the dummies) that if I need to install AmberTools13, I have to start from
> scratch the whole process of installing Amber11 and CUDA??? If it's true,
> oh god, a nightmare!!!
>
No, you will not have to reinstall all of Amber 11. In fact, it's a
separate install altogether. See this page for instructions on how to
install 'new' AmberTools alongside 'old' Amber:
http://jswails.wikidot.com/installing-ambertools-13-and-older-amber
Using MMPBSA.py may solve your problem, or if there is something very wrong
it may provide a more intuitive error message.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 11 2013 - 06:00:03 PDT
