[AMBER] Amber parmeters for ACE-CYX bond

From: Ali Kusay <Ali.Kusay.anu.edu.au>
Date: Wed, 4 Aug 2021 04:59:41 +0000


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?


Ali Kusay

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Received on Tue Aug 03 2021 - 22:30:02 PDT
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