Hi Jason,
Yes, this is exactly what I need. It works for me. Thanks!
Best,
Wei
On Mar 25, 2011, at 9:56 AM, Jason Swails wrote:
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Mar 25 2011 - 08:30:05 PDT
