Hi,
I just added a new command 'keep' to github cpptraj that should do
what you want: https://github.com/Amber-MD/cpptraj/pull/957
Let me know if it works for you.
-Dan
On Mon, Mar 14, 2022 at 10:21 PM Rakesh Srivastava
<allahabad.21.gmail.com> wrote:
>
> Thanks Dan for your kind support. I will use your suggestions.
>
> *Rakesh Srivastava, Ph.D.*
> Postdoctoral Fellow
> Center for Computational Natural Sciences and Bioinformatics (CCNSB)
> International Institute of Information Technology, Hyderabad, India
>
>
>
> On Mon, Mar 14, 2022 at 8:50 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Sat, Mar 12, 2022 at 12:14 AM Rakesh Srivastava
> > <allahabad.21.gmail.com> wrote:
> > >
> > > Dear Amber users, for a MMPBSA calculation, I want those explicit water
> > > molecules to be kept in the trajectory which form a bridged H-bond
> > between
> > > protein and ligand, while the rest of other water molecules to be
> > stripped.
> >
> > So right now there's no way to do this directly (but it's a good idea
> > and functionality I'd like to add). For now, the information you need
> > is in the [ID] data set (bridging ID) created by 'hbond' and written
> > to the 'out' file (restrict 'hbond' to only the solute residues you
> > are interested in). The bridging ID data set is a string and contains
> > 'None' if there are no bridging waters and a string with format
> > ’<solvent resnum>(<solute res1>+<solute res2>+...+),...’ otherwise.
> > For example:
> >
> > 208(10+11+)
> >
> > Means solvent residue 208 bridged solute residues 10 and 11. That
> > would be the residue you want to keep for that frame; right now you'd
> > have to strip everything else out manually.
> >
> > I'll keep you updated if I think of a better solution.
> >
> > -Dan
> >
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Received on Wed Mar 16 2022 - 13:30:02 PDT
