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 Mon Mar 14 2022 - 19:30:02 PDT
