Re: [AMBER] How to generate Phi_Psi by cpptraj ?

From: James Maier <jimbo.maier.gmail.com>
Date: Mon, 1 Jun 2015 15:44:35 -0400

You need the trajin and dihedral commands. Assuming the residue you want
phi and psi for is stored in variable $res and the parmtop file is in
variable $parmtop:

cpptraj $parmtop << EOF
trajin prod.nc
dihedral Phi :$((res-1)).C $res.N $res.CA $res.C out ${res}_Phi_Psi.dat
dihedral Psi $res.N $res.CA $res.C $((res+1))@N out ${res}_Phi_Psi.dat
go
EOF

will store <frame> <phi> <psi> in the file ${res}_Phi_Psi.dat

On Mon, Jun 1, 2015 at 3:27 PM, Michael Shokhen <michael.shokhen.biu.ac.il>
wrote:

> Dear Amber List members,
>
> What is a cpptraj command for generation Phi_Psi two columns file
> using aMD trajectory prod.nc file as input ?
>
> Thank you,
> Michael
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: michael.shokhen.gmail.com
> email: shokhen.mail.biu.ac.il
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 01 2015 - 13:00:03 PDT
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