Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture

From: Daniel Roe <>
Date: Tue, 2 May 2017 13:45:28 -0400


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,


On Thu, Apr 27, 2017 at 4:21 AM, Marcel Passon <> 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]
> Thank you very much for your help!
> References
> 1.
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
AMBER mailing list
Received on Tue May 02 2017 - 11:00:03 PDT
Custom Search