Hi,
Unfortunately I'm not able to access the link you posted due to
security restrictions. If the files are not too big can you send them
to me off-list so I can try to reproduce the issue? Otherwise you can
post the complete output from cpptraj and I can try to troubleshoot
from there. Thanks,
-Dan
On Thu, Apr 27, 2017 at 4:21 AM, Marcel Passon <passonmarcel.web.de> wrote:
>
> Dear Amber users,
>
>
> I’m still not quite familiar with using CPPTRAJ. So I tried to calculate the
> overall SASA of a protein that I’ve simulated in a solvent-mixture of
> acetonitrile and water with the ‘surf’ command. Strangely, at the beginning
> of the trajectory, the output gave very low areas, that increased to the end
> from 1125 to 14488 (in VMD, the protein doesn’t seem to unfold or change its
> conformation notably). Could this be because the acetonitrile molecules
> aren’t recognized as solvent (when I did the same in pure water as solvent,
> the values remained quite similar)?
>
>
> In my fileshare link you can get the first frame of my trajectory, its
> parameter file as well as the ‘surf’ output file for the simulation in the
> solvent mixture (surfACE.dat) and in pure water (surf.dat):
>
> [1]http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ
>
>
> Thank you very much for your help!
>
> References
>
> 1. http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue May 02 2017 - 11:00:03 PDT
