Hello,
I would like some help parameterising this peptide fragment (
https://imgur.com/LumK7Wh). This features an unusual bond between the CH3 atom of ACE and sulphur atom in cysteine, I could not find previous forums with advice on this.
I know that I can use the bond command in tleap to bond ACE-CH3 and S-CYX, but there in an extra hydrogen from ACE-CH3 that needs to be removed for this to work. I think that I also need to reassign partial charges for the ACE-CYX residues?
Could anyone please provide some advice on what to do to achieve this?
Cheers,
Ali Kusay
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 03 2021 - 22:30:02 PDT
