On 24/01/2012 8:39 AM, Li, Hualin wrote:
Hi,Mark,
Thank you very much for your answer. In this case , if I want to know
about the protein structure(like bonding, angles...), Is there any method I can
use please?
g_bond and g_angle allow you to measure bond lengths and angles of atoms
in well chosen index groups.
The difficult part in this question may be that I have more than one proteins
in the same output file(GRO), I know some tcl script may draw the protein
structure in CG model (including bonding and secondary structures) one protein
by one protein, but is there any method to draw the structure for all the
proteins at the same time?
With suitable modification to their heuristics for guessing where bonds
occur, various visualization packages can be useful. The GROMACS webpage
has some suggestions.
Mark
Thanks again.
--Hualin
________________________________________
From: [email protected] [[email protected]] On Behalf
Of Mark Abraham [[email protected]]
Sent: Monday, January 23, 2012 3:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PSF file in martini force field
On 24/01/2012 4:20 AM, Li, Hualin wrote:
Hi all,
I am running Gromacs on the system of several proteins on the membrane
using martini force field.From the output files, if I want to generate the PSF
files from them , is there any easy way to do it please?
No GROMACS utilities will write a PSF for CHARMM input. Consult the
CHARMM documentation.
Mark
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