Hi,
thank you very much for your advice! Indeed, after stripping the atoms that
are not calculated, it worked and I obtained a realistic result (from 13500
to 16900).
I'll also consider using the 'molsurf' command.
Thanks!
Marcel
Gesendet: Donnerstag, 04. Mai 2017 um 17:54 Uhr
Von: "Daniel Roe" <daniel.r.roe.gmail.com>
An: "AMBER Mailing List" <amber.ambermd.org>
Betreff: Re: [AMBER] Error with 'surf' and acetonitrile-water solvent
mixture
PS - You can also try the 'molsurf' command, which uses a better
procedure for the surface area calculation.
On Thu, May 4, 2017 at 11:00 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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][1]http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ
>>>
>>>
>>> Thank you very much for your help!
>>>
>>> References
>>>
>>> 1. [2]http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> [3]http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> [4]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
> [5]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
[6]
https://www.lobos.nih.gov/lcb
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AMBER mailing list
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[7]
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References
1.
http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ
2.
http://jmp.sh/b/qmIfZACyYNMwuTqsT6wJ
3.
http://lists.ambermd.org/mailman/listinfo/amber
4.
https://www.lobos.nih.gov/lcb
5.
https://www.lobos.nih.gov/lcb
6.
https://www.lobos.nih.gov/lcb
7.
http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri May 05 2017 - 08:00:03 PDT
