Hello Dan,
Thanks a lot for your helps. I try to run cpptraj from github by command
line:
cpptraj -i cptrj.in -p protein.prmtop
but it always failed with messages:
Warning: No numerical value, line 1110134 column 2. Skipping.
Warning: No numerical value, line 1110145 column 2. Skipping.
Warning: No numerical value, line 1110156 column 2. Skipping.
Warning: No numerical value, line 1110167 column 2. Skipping.
Warning: No numerical value, line 1110179 column 2. Skipping.
100000 frames
TIME: Total execution time: 36.2845 seconds.
Here is my cptraj.in file:
readdata output/remd.mdout.0* separate name Out
runanalysis multihist out hist.eptot.agr normint bins 200 Out*[EPtot]
It doesn't generate any output file....
Thanks again for helps.
Albert
On 10/20/2017 03:39 PM, Daniel Roe wrote:
> Assuming that the plot you reference has potential energy histograms,
> you can do this easily using the GitHub version of cpptraj, e.g.:
>
> readdata OUTPUT/rem.out.0* separate name Out
> runanalysis multihist out hist.eptot.agr normint bins 200 Out*[EPtot]
>
> See the manual for full options of 'multhist' etc.
>
> mdout_analyzer.py may also have options to do this.
>
> -Dan
>
> On Fri, Oct 20, 2017 at 7:17 AM, Albert <mailmd2011.gmail.com> wrote:
>> Hello,
>>
>> I have finished a REMD in Amber. I am just wondering how can we generate
>> data for the following plot in Amber:
>>
>>
>> http://www.gromacs.org/.api/deki/files/210/=combined-pot.jpg
>>
>>
>> This would be very helpful to check the quality of our simulation. My
>> another question is: how shall we select a conformation which is
>> presented in all simulation for analysis?
>>
>>
>> thank you very much.
>>
>> Albert
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Oct 25 2017 - 12:00:03 PDT
