> CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.12)
PS - I highly recommend updating to the latest CPPTRAJ from AmberTools
23 or GitHub (
https://github.com/Amber-MD/cpptraj). The one you are
using is several years old.
-Dan
On Wed, May 10, 2023 at 8:41 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> On Sat, May 6, 2023 at 1:55 AM Dulal Mondal
> <babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> > Acceptor-only atoms: 0
> > Donor/acceptor sites: 0
> > Donor-only sites: 0
> > 0 solute hydrogens.
> > Solvent sites (16266)
> > 0 solvent hydrogens, 0 ions.
> > Estimated max potential memory usage: 0.144 kB
>
> So according to this, nothing is being selected by the masks you are
> providing. You can test out mask expressions beforehand using the
> 'select' command, e.g.:
>
> parm ../ambercpin.prmtop
> select :259.ZN
> select :WAT.O
>
> And so on. If nothing is printed for the above expressions, then you
> need to change them. Do you have water residues named WAT? I know that
> for example in CHARMM it's common to have water residues named TIP3.
>
> Hope this helps,
>
> -Dan
>
> >
> > Thanking you
> >
> > On Sat, May 6, 2023 at 12:31 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> Probably your best bet would be to use the 'hbond' command with
> >> 'series' and 'solventacceptor :WAT.O' keywords to generate time series
> >> data for waters interacting with the Zn (make sure the distance cutoff
> >> is set to around 3.5, set angle cutoff to -1 to disable), followed by
> >> 'lifetime' analysis to measure the lifetime of 'bound' states. See the
> >> manual for full command details. A very very basic example of this is
> >> given in the following tutorial:
> >> https://amberhub.chpc.utah.edu/hydrogen-bond-analysis-within-a-protein/
> >>
> >> Maybe others have a better idea. Hope this helps,
> >>
> >> -Dan
> >>
> >> On Wed, May 3, 2023 at 10:19 AM Dulal Mondal via AMBER
> >> <amber.ambermd.org> wrote:
> >> >
> >> > Dear Users,
> >> >
> >> > I have a trajectory and a prmtop file. I am trying to calculate the
> >> > residence time of water molecules.
> >> > How long do water molecules remain in a sphere of radius 3.5 angstrom
> >> > centered from the Zn atom?
> >> >
> >> > Thanking you
> >> >
> >> >
> >> >
> >> > --
> >> > *With regards,*
> >> > *Dulal Mondal,*
> >> > *Research Scholar,*
> >> > *Department of Chemistry,*
> >> > *IIT Kharagpur, Kharagpur 721302.*
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed May 10 2023 - 18:00:02 PDT
