Hi Ray,
That’s actually the part that surprised me: My system is a <150 residue helix bundle protein with two heme groups. I only get the error related to maxarcdot when trying to use an implicit membrane. Could that somehow be related?
I notice that the implicit membrane, when visualized by printing the level set function, looks like a blob (see attached). Is this what it should look like? The example int eh manual looks more rectangular.
Thanks again for the help; I deeply appreciate it!

Best,
Matthew
> On Nov 15, 2023, at 8:52 PM, Ray Luo <rluo.uci.edu> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Matthew,
>
> I can't recommend anything out of the blue. You may add 250 each time
> to see when it goes away. Apparently, the consequence of using a
> larger number would drive up memory usage. There is no other effect on
> the computation.
>
> You probably have a system whose packing is different from proteins.
> It could also be due to the presence of many atoms with large radii.
>
> 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 4:12 PM Matthew Guberman-Pfeffer
> <matthew.guberman-pfeffer.uconn.edu <mailto: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%7C3bc44cb73bf94ca3abde08dbe646ca54%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638356963936851278%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XEPTZbK%2BH1Xmqi369JApzOB3YUS8vXzxY83dWlpHWfY%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 - 18:30:03 PST
