I am not sure what you did in cpptraj, but I do not see a gnu file as
output there.
Anyways, the file you sent with extension .gnu is NOT a gnuplot file, is
is a regular data file with no gnuplot commands. That is why you got an
error
adrian
On 8/11/16 12:16 PM, Parviz Seifpanahi Shabane wrote:
> Sure, Thank you for your help, I will be grateful if you help me about my
> second question too.
> secondarystructuer-folded-ff10.gnu
> <https://drive.google.com/a/vt.edu/file/d/0BwxMdQ596dWgdndfN0dVZ0ZXSlE/view?usp=drive_web>
>
>
> On Thu, Aug 11, 2016 at 12:05 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> 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 ?
>>
>> Thanks
>>
>>
>>
>> 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 1WJB-OPC-FF10-folded.top
>>> 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
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> Dr. Adrian E. Roitberg
>> University of Florida Research Foundation Professor.
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Aug 11 2016 - 09:30:04 PDT
