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
