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-- 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 4:12 PM Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu> wrote: > > 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 > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber__%3B!!CzAuKJ42GuquVTTmVmPViYEvSg!M_sE739oXyJHj761ZXLacoC02jUOzCaTzaQ54kOXQHaOH8RCh9a8HiGWGvKWQm6Wj8lxi_CJxGU%24&data=05%7C01%7Cmatthew.guberman-pfeffer%40uconn.edu%7C737d8709b1c8403e978508dbe632f620%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638356878772497240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=V5OJdw%2Fp4ubf7Q76GUONviuZMVE8DnmC%2F2WZ0Xsi9bI%3D&reserved=0 > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7Cmatthew.guberman-pfeffer%40uconn.edu%7C737d8709b1c8403e978508dbe632f620%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638356878772497240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=AWJtAADXkOsQaGSVuusZj5ec5hhbMLDVpQCT5Cv8zRc%3D&reserved=0 > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Nov 15 2023 - 18:00:02 PST