[gmx-users] Re: phi/psi (For Raj)

[Kia.Balali-Mood@ed.ac.uk]

Hi Raj

Have u used g_helix, sounds as if it could be useful. Two output files are 
phi.xvg and psi.xvg. make sure u have an index file with ur peptide isolated. 
The out put is average phi/psi angles for the whole peptide over the course of 
ur sim. 

best of luck

Kia

> > > On Sat, 2004-01-17 at 18:46, Raj Badhan wrote:
> > > > Dear All,
> > > > I've tried many option within gromacs to get what i want, and i'm 
> > > > confused to bits now.
> > > > I want to calculate the Phi/Psi angles average over a certain time.
> > > > I need these to be in one file and not for the program to calculate 
> > > > the Phi/Psi angles for every amino acid.
> > > 
> > > if you just want specific phi/psi for a few residues than you can make
> > > an index file for your angles and then use g_angle.
> > > 
> > > > I've tried g_chi/g_angles/g_dih etc. and no luck.
> > > > Hope someone could offer some help with this!!!
> > > > Many thanks
> > > > Raj Badhan
> > > > Postgraduate researcher
> > > > School of Pharmacy and Pharmacetical Science
> > > > The University of Manchester
> > > > Manchester, UK.
> > > > _______________________________________________


******************************************************************************
Kia Balali-Mood
Laboratory of Membrane Biophysics
Division of Pre Clinical Veterinary Sciences
University of Edinburgh
College of Medicine & Veterinary Medicine
The Vet School
Summerhall
Edinburgh, EH9 1QH
Tel. +44 (0)131 650 6142
Fax. +44 (0)131 650 6576
leaflet.vet.ed.ac.uk