I chose a distance-based mask using the mask command.
mask "(:ZN6<:8.0)&:WAT,WT1" maskout wat.dat maskpdb wat.pdb name tr
It generates 1000 pdb files. Then I perform matrix and diagmatrix commands.
parm wat.pdb.1
trajin wat.pdb.1
matrix name entropy mwcovar :WAT,WT1 out watcorel1.dat
diagmatrix entropy out entropy1.dat thermo outthermo thermo1.dat
go
But it shows the following error. It does not generate any therno1.dat file.
Error: DataSet_Modes: bad eigenvalue 0 = 0.000000
Error: In Analysis [diagmatrix]
Thanking You
On Mon, Dec 18, 2023 at 5:56 PM Dulal Mondal <
babunmondal.chem.kgpian.iitkgp.ac.in> 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.*
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Mon Dec 18 2023 - 06:00:02 PST
