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 - 08:30:02 PDT
