Hi,
It took a while for me to get to it, but this issue in cpptraj is now
fixed in GitHub: https://github.com/Amber-MD/cpptraj/pull/506
Thanks again for the report.
-Dan
On Fri, May 5, 2017 at 10:43 AM, Marcel Passon <passonmarcel.web.de> wrote:
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> [7]http://lists.ambermd.org/mailman/listinfo/amber
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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
https://www.lobos.nih.gov/lcb
_______________________________________________
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Received on Mon Jul 03 2017 - 12:30:02 PDT
