Re: [AMBER] {SPAM?} Force filed for non-specific residue CAS

From: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
Date: Tue, 15 Nov 2022 21:53:03 -0500

S-(dimethylarsenic)cysteine is a non-standard (not “non-specific”) amino acid. Your choice is to either find parameters in the literature or to develop parameters yourself. Googling "AMBER, parameterize non-standard residue” returns some great references for a starting place.

I hope that helps.

Best,
Matthew


> On Nov 15, 2022, at 7:07 PM, Jelena Tosovic via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hello,
>
> I would like to run MD simulation for the protein system which
> consists non-specific residue CAS (S-(DIMETHYLARSENIC)CYSTEINE). tLeap
> doesn't recognise this amino acid residue.Where can I find the designation
> for CAS amino acid which tLeap will recognize?
>
> Best regards,
> Jelena
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&amp;data=05%7C01%7C%7C8ae7bbbe508a4c7ae55208dac766a571%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638041540923709398%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=3K2AyWTTr8WgQULq8y8aLOeqOsD6vRgbru6m%2FsNFO%2BU%3D&amp;reserved=0


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 15 2022 - 19:00:03 PST