g_angle will do that fine, and with the options you used it should have done
so. Possible issue that may make that fail is you failed to generate the
correct angle index file for the dihedral(s) of interest.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
________________________________
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Venkat Reddy
Sent: Wednesday, 1 April 2009 7:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to calculate the dihedral angle variations
???
Hai Sir !
Actually i want to see the dihedral angle (Cβ-S-S-Cβ) variation over
time.I used the commands
"g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od
angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg
-type dihedral -all"
"g_chi -s gp123_full.gro -f gp123_full.trr -o order.xvg -jc
Jcoupling.xvg -g chi.log -rama -all"
Please suggest me the right options
Thanks for ur concern
2009/4/1 Tsjerk Wassenaar <tsje...@gmail.com>
Hi Venkat,
What exactly do you mean with variations. Do you want to follow
the
angle over time, or do you want distributions with mean and
variance
estimates? g_angle and g_chi seem to be the appropriate tools.
You
mention you tried all suitable options, but fail to explain
what you
tried and what exactly it is you want. We need that sort of
information to be able to help you out.
Cheers,
Tsjerk
2009/4/1 Venkat Reddy <venkat...@gmail.com>:
> First of all Thanks for ur reply !
> I tried both g_angle and g_chi with all suitable options, but
i didn't get
> the required result.Can u plz help me in this regard ???
>
> 2009/4/1 Antonia V. <antonia_h...@hotmail.com>
>>
>> Did you try g_angle??
>>
>> Antonia
>> ________________________________
>> Date: Wed, 1 Apr 2009 11:35:29 +0530
>> From: venkat...@gmail.com
>> To: gmx-users@gromacs.org
>> Subject: [gmx-users] How to calculate the dihedral angle
variations ???
>>
>> Hi Everyone !
>> How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide
bridge)
>> dihedral angle during a simulation ?????
>> Thanks in advance
>>
>>
>>
>> Cheers from
>> Venkat Reddy Chirasani
>> M.Tech Bioinformatics
>> UNIVERSITY OF HYDERABAD
>>
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>
>
> --
> Venkat Reddy Chirasani
> M.Tech Bioinformatics
> UNIVERSITY OF HYDERABAD
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD
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