Hi,
I'm not sure why you're using the 'thermo' analysis from diagmatrix
for calculating water entropy - that's the wrong tool for the job.
It's really important that you read up on these methods before you use
them; it shouldn't be treated like a "black box". You really want
something like GIST (the 'gist' command in cpptraj). Check the manual
and assorted literature, and check out the GIST tutorial
https://ambermd.org/tutorials/advanced/tutorial25/. That should be
enough to get you started.
Hope this helps,
-Dan
On Mon, Dec 18, 2023 at 7:26 AM Dulal Mondal via AMBER
<amber.ambermd.org> wrote:
>
> Dear Experts,
>
> I am trying to calculate the entropy of the active site water molecules
> using cpptraj.
> I select active site water molecules using the following mask
> :ZN6<:10.0&:WAT,WT1
> parm *.prmtop
> trajin *.nc
> matrix name entropy mwcovar :ZN6<:10.0&:WAT,WT1 out watcorel.dat
> diagmatrix entropy out entropy.dat thermo outthermo thermo.dat
> go
> But it shows the following error.
> Error: No reference set, cannot select by distance.
>
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 18 2023 - 07:00:02 PST
