[gmx-users] How to calculate the dihedral angle variations ???

[Dallas B. Warren]

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.warren at 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-bounces at gromacs.org [mailto:gmx-users-bounces at 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 <tsjerkw at 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 <venkat4bt at 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_haha at hotmail.com>
		>>
		>> Did you try g_angle??
		>>
		>> Antonia
		>> ________________________________
		>> Date: Wed, 1 Apr 2009 11:35:29 +0530
		>> From: venkat4bt at gmail.com
		>> To: gmx-users at 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.
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	-- 
	Venkat Reddy Chirasani
	M.Tech Bioinformatics
	UNIVERSITY OF HYDERABAD
	

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