Hi,
Thanks for the files. I am seeing some weird behavior of the 'surf'
command with them so I think there is a bug lurking in there. For now
a potential workaround may be to 'strip' all atoms you do not want to
calculate the surface area for, e.g.
parm HY133_ace_noions.prmtop
trajin HY133_ace_noions_prd.nc
strip !(:10001-10281)
surf out surfACE.dat
run
Let me know if that helps. In the meantime I'll try to figure out
what's going wrong. Thanks for the report,
-Dan
On Tue, May 2, 2017 at 1:45 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
--
-------------------------
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 Thu May 04 2017 - 08:30:02 PDT
