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

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Mon, 1 Jun 2015 22:41:11 +0200

Its something like that

trajin md1_dry.nc
#dihedral angle
dihedral phi .1205 @535 @3334 @4451 out phi1.dat
dihedral psi .1205 @535 @3334 @4451 out psi1.dat

Note . denotes atom number. I choose the atom number of CA of a certain
residue. Hope it helps.

/SB

On Mon, Jun 1, 2015 at 9:44 PM, James Maier <jimbo.maier.gmail.com> wrote:

> 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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-- 
Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Homepgae: https://cbiores.wordpress.com/
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Mon Jun 01 2015 - 14:00:02 PDT
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