There is a nice routine called ante-MMPBSA.py (e.g., in the AmberTools12
manual, p259) that can be used to prepare the required files.
Pete
On 7/26/13 10:41 AM, "siddharth kesharwani"
<siddharthnipermohali.gmail.com> wrote:
>No need to remove water tou can perform the calculations using water
>On 26 Jul 2013 08:19, "Shashidhar Rao" <shashidharr.gmail.com> wrote:
>
>> Hello AMBER Gurus,
>>
>> I apologize for asking a very naive question. I have carried out AMBER
>>MD
>> studies on a series of protein-ligand complexes and would like to carry
>>out
>> MMGB-SA and MMPB-SA calculations on the trajectories. my system
>>includes a
>> box of waters in addition to the protein-ligand complex as well as the
>> counterions. I wanted to know if the MMPBSA.py script can be run on the
>> trajectories as they are or do I need to take out the waters and the
>> counterions. If latter, what is the best way to do so (perhaps
>>cpptraj)?
>>
>> thanks for your help in advance,
>> Shashi Rao
>>
>> --
>> Shashidhar N. Rao
>> 3 SERINA DRIVE
>> PLAINSBORO
>> NEW JERSEY 08536 USA
>>
>> shashidharr.gmail.com
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>>
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Received on Fri Jul 26 2013 - 08:00:09 PDT
