I forgot -- how to use it: Edit the head of the file (it should be pretty
straightforward), then run the script with now arguments in the folder with
the _MMPBSA_*mdout files you want too analyze.
Hope this helps,
Jason
On Fri, Mar 25, 2011 at 7:54 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hi Wei,
>
> I wrote a little script that stops *just* short of this. It extracts all
> of the energies for each snapshot and dumps them to a file. Then you can
> use a simple awk command and take each difference (each line has the energy
> values on a single line:
>
> complex receptor ligand
>
> ). I've attached it to this email. Is this the type of thing you were
> talking about? You do have to make sure that keep_files = 1 as Dwight said
> (which is the default value).
>
> All the best,
> Jason
>
> On Fri, Mar 25, 2011 at 7:18 AM, Wei Huang <whuang.cct.lsu.edu> wrote:
>
>> Dear Amber Users,
>>
>> I am going through the tutorials using MMPBSA.py to calculate binding free
>> energy. I wonder how I can extract binding free energy for each snapshot
>> using this module. Is there any script available to do this?
>>
>> Thanks,
>> Wei
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
>
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 25 2011 - 08:00:04 PDT
