Thanks Dan for sharing the link. Sure, I will use it.
Thanks.
*Rakesh Srivastava, Ph.D.*
Postdoctoral Fellow
Center for Computational Natural Sciences and Bioinformatics (CCNSB)
International Institute of Information Technology, Hyderabad, India
On Thu, Mar 17, 2022 at 1:37 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 Thu Mar 17 2022 - 02:00:02 PDT
