Re: [AMBER] secondary structure graph vs Time

From: Adrian Roitberg <>
Date: Thu, 11 Aug 2016 12:05:01 -0400

Dear Parviz.

First, that seems like a gnuplot question, not amber. Second, can you
attach the .gnu file so we can see what is happening ?


On 8/11/16 12:03 PM, Parviz Seifpanahi Shabane wrote:
> Dear Amber User,
> I need to calculate the secondary structure(Para+Anti+Alpha+3-10+Pi) of my
> protein vs time.I used this script (below).
> parm
> trajin 1WJB-OPC-FF10-folded.prod1.traj
> secstruct :1-55 secstr-folded-ff10.dat out
> secondarystructuer-folded-ff10.dat sumout average-folded-ff10.dat assignout
> overall-folded-ff10.dat
> and I got the file (secondarystructuer-folded-ff10.gnu), in this file each
> kind of secondary structuer show with the number, I used the " gnuplot
> secondarystructuer-folded-ff10.gnu" to see the graph and I got this error
> "secondarystructuer-folded-ff10.gnu", line 2: invalid command".
> dose any one knows what is the problem?
> and how to get the graph (secondary structure(Para+Anti+Alpha+3-10+Pi) vs
> time)?
> Best Regrads
> Parviz
> _______________________________________________
> AMBER mailing list

Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
AMBER mailing list
Received on Thu Aug 11 2016 - 09:30:03 PDT
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