Many thanks for all the help !
Just to add, I also found chimera really easy to process output data.
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Thursday, January 08, 2015 10:07 AM
To: AMBER Mailing List
Subject: Re: [AMBER] extract torsion angle data
Hi,
Just to add to Jason's excellent reply, you actually can define custom
dihedral types with the 'multidihedral' command using the 'dihtype'
keyword:
[dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>] ...]
Offset -2=<a0><a1> in previous res, -1=<a0> in previous res,
0=All <aX> in single res,
1=<a3> in next res, 2=<a2><a3> in next res.
For example, to search for a dihedral type named chi1 using atoms N,
CA, CB, and CG:
multidihedral dihtype chi1:N:CA:CB:CG out custom.dat
-Dan
On Thu, Jan 8, 2015 at 6:28 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, 2015-01-08 at 07:34 +0000, Anupam Goel wrote:
>> Hi all,
>>
>> I am looking to extract torsion angle information from my MD runs,
>> does anyone know where to find a good tutorial for that? I did find
>> steps to obtain Trp phi psi angles among amber analysis tutorials but
>> it would be great to obtain torsion angles for all residues in
>> peptide.
>
> Look at the "multidihedral" command in cpptraj. It will allow you to
> compute the phi, psi, chi_p, omega, alpha, beta, gamma, delta, epsilon,
> zeta, nu_1, nu_2, and/or chi_n dihedrals for protein and/or nucleic acid
> residues. It will compute all of them for the residues in the range of
> your choosing.
>
> You can type "help multidihedral" in cpptraj to get a printout of the
> help or you can look at the description in the Amber 14 manual.
>
> If the dihedral you want to compute is *not* one of those common ones,
> you will need to write a script to use the "dihedral" command for each
> dihedral you want to analyze separately.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jan 08 2015 - 15:00:02 PST
