Hi Mondal,
a very quick guess: Since your mask is distance dependent, you need to
specify a reference structure on which the atom mask is evaluated, see the
reference command in ptraj, manual section 35.10.3.
There is another potential issue in case you expect the mask to be dynamic
("any oxygen that happens to come close to the Zn during the simulation").
Since the correlation matrix has to have a fixed width, I dont think this
will work if the oxygen atom (or atoms, since the number close to Zn can
change during the course of the trajectory) in question is not always the
same. It may be safer to explicitly specify one oxygen you care about by
e.g. residue or atom number.
Kind Regards,
Thomas
On Tue, Apr 18, 2023 at 2:45 PM Dulal Mondal via AMBER <amber.ambermd.org>
wrote:
> Dear Users,
>
> I am trying to calculate the Correlation matrix using the matrix command
> using cpptraj.
> parm *.prmtop
> trajin average.pdb (I generate this pdb using the average command)
>
> matrix correl :1-258 :ZN6<:2.55&:WAT&!.H= out cor7.dat byres
>
> After running those command I fet following error.
>
> Error: No reference set, cannot select by distance.
> Mask [:ZN6<:2.55&:WAT&!.H*] corresponds to 1 atoms.
>
> I am trying to calculate correlation matrix between protein residues and
> the O atom that appear wiin 2.5 angstrom from the zinc.
>
> Thanking you
>
>
>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
> _______________________________________________
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Tue Apr 18 2023 - 06:00:02 PDT
