On Wed, Sep 14, 2016 at 6:06 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
wrote:
> Hi,
>
> I am trzying to calculate binding energy between two proteins using MMPBSA
> method. I found that all ions were automatically deleted by ptraj. However,
> I want to keep Mg2+ intact in my system. How can I do this.
>
Two options:
1. Set the strip_mask variable to explicitly omit the ion you want to keep
2. Pre-process the trajectory with cpptraj first to prevent MMPBSA.py from
stripping any solvent
HTH,
Jason
--
Jason M. Swails
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Received on Wed Sep 14 2016 - 09:00:03 PDT
