Dear Jason,
Thank you for the reply.
By the way, just FYI, I ran again the mmpbsa calculation (before receiving
your reply), but I disabled the PB calculation (PB =0, GB =1). The process
last longer (finished all the 100 snapshot_com.crd.*, but terminated at
snapshot_rec.crd.1), and again no specific error was shown.
I will install the new AmberTools as you instructed. Thanks.
Any further help/suggestion is always appreciated.
Regards,
Chinh
On Tue, Jun 11, 2013 at 8:38 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
>
> 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 - 21:00:02 PDT
