Hi,
The command you want is 'matrix mwcovar' in cpptraj. Something like:
parm <pdbfile>
trajin <xtc>
matrix mwcovar name MyMatrix <other keywords> out mymatrix.dat
run
Please see the manual for full details on all commands. You may also
be interested in the 'modes' and 'diagmatrix' commands for further
analysis.
However, be aware that since your PDB is not really a topology file,
cpptraj will assign default masses based on the elements detected in
the PDB.
-Dan
On Wed, Feb 2, 2022 at 9:55 AM gmx <qasimpars.gmail.com> wrote:
>
> Dear users,
>
> I have a reference .pdb file and .xtc trajectory file of a protein. I need to generate the mass-weighted covariance matrix but I don't know how to do it with Amber. Can someone tell me how I can get the mass-weighted covariance matrix with Ambertools?
>
> Thanks in advance.
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Received on Wed Feb 02 2022 - 08:00:03 PST
