Dear Dan,
Thank you for your help. Yes, the errors are innocuous because the calculation is still progressing.
Sylvester
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, March 24, 2015 3:02 PM
To: AMBER Mailing List
Subject: Re: [AMBER] concave edge on torus has mismatched atoms
Hi,
These errors are from the surface area calculation (molsurf command).
Essentially the algorithm didn't like something about those frames and
couldn't determine a continuous surface. They are largely innocuous,
just ignore the frames for which that happens (the surface area for
these will be abnormally small or -1). You can also try changing the
probe radius a bit and/or increasing the offset to see if that helps
those frames, but its probably not necessary.
Note these shouldn't be fatal errors (i.e. the calculations should
continue). Let me know if they are.
-Dan
On Tue, Mar 24, 2015 at 1:28 PM, Sylvester Tumusiime <stumusii.uno.edu> wrote:
>
> Dear Amber users,
> I have run a cpptraj command to trajin my netcdf files, trajout a composite
> netcdf file and then determine radial distribution, hbonding, molecular
> surface area and energy in my system.
> I have looked in my output file and i see the following error:
>
> ----- [prod3.netcdf] (1-1000, 1) -----
>
> 0% concave edge on torus has mismatched atoms
>
> torus 11 atoms 0 13
>
> edge 22 vert1.atom 4 vert2.atom 13
>
> concave edge on torus has mismatched atoms
>
> torus 11 atoms 0 13
>
> I would appreciate any help with this.
>
> Thank you very much,
>
> Sylvester
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 24 2015 - 13:30:04 PDT
