Hi Jason,
The earlier incarnation of MMPBSA.py had a strip_mdcrd command that could be set to 0 “Do not strip strip_mask from the initial trajectory”.
I guess this is not applicable with AmberTools 13.
Regards
George
On Feb 27, 2014, at 4:44 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, 2014-02-27 at 16:27 -0300, George Tzotzos wrote:
>> Thanks Jason.
>>
>> The water molecule that comprises part of the solute is numbered as residue 127
>>
>> One of the default values of the strip_mask is is :WAT. How can one
>> set the strip_mask for all water molecules except the one that is part
>> of the solute (residue 127)?
>
> Maybe something like
>
> strip_mask = ':WAT,Na+,Cl-&!:127'
>
> You can use parmed.py or cpptraj to check that these masks select the
> atoms you want to select.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu Feb 27 2014 - 12:30:03 PST
