Re: [AMBER] PBSA error

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Wed, 15 Nov 2023 19:11:40 -0500

Ray,

Thank you so much for the reply! What is a reasonable range of values? Is there any harm in making maxarcdot too large? And, why would the number per atom need to be larger. I’d like to understand a bit about what this setting and issue means. Can you please help me understand this points.

Best,
Matthew


On Nov 15, 2023, at 6:29 PM, Ray Luo via AMBER <amber.ambermd.org> wrote:

*Message sent from a system outside of UConn.*


Matthew,

This issue was fixed in the source code last time. You can now set the
keyword "maxarcdot" in the pb control name list. The default is 1500
per atom. Looks like you'll have to set it to a larger number for your
system.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Wed, Nov 15, 2023 at 12:44 PM Matthew Guberman-Pfeffer via AMBER
<amber.ambermd.org> wrote:
Dear Amber community,
I get the the following error when trying to run PBSA with an implicit membrane slab:
SA Bomb in circle(): Stored surface points over limit******
A similar issue was reported nearly 20 years ago (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Farchive.ambermd.org%2F200504%2F0365.html__%3B!!CzAuKJ42GuquVTTmVmPViYEvSg!M_sE739oXyJHj761ZXLacoC02jUOzCaTzaQ54kOXQHaOH8RCh9a8HiGWGvKWQm6Wj8lxHhMqMkY%24&data=05%7C01%7Cmatthew.guberman-pfeffer%40uconn.edu%7C737d8709b1c8403e978508dbe632f620%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638356878772497240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hlgF2n4oDfpEjpMDjzlm%2FlSZnLG6eRay0RoKbVTLqdo%3D&reserved=0 ), but a resolution was not given. Can any one please help me resolve this problem?
Best,
Matthew
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Received on Wed Nov 15 2023 - 16:30:03 PST