Re: [AMBER] Thioester Bond Parameters

From: Dr. Anselm Horn via AMBER <>
Date: Mon, 6 Nov 2023 18:46:29 +0100


your approach sounds reasonable; you may have to constrain the total
charge of the groups to 0, and could also use charge constraints for the
peptide atoms in capped cysteine to be consistent with the rest of the
force field. (One could even use two different conformations, i.e. alpha
and beta, for the capped cysteine.)

Maybe the authors of the following publication (I just have read the
abstract) can provide further suggestions:



Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

Am 06.11.2023 um 17:44 schrieb Shah, Tejas V. via AMBER:
> Hello AMBER users,
> For one of my projects, I have to model cysteine sulfur and glycine carbonyl thioester bond. I looked at the PyRED served tutorial, and from my understanding, I have to cap NH2 and COO of CYS with conventional NME and ACE cap groups. I also have to cap cysteine S with COO-CH3 and GLY COO-with S-CH3 and remove them in my project config file with no Intra and Inter charge. The obtained mol2 files will then be taken to parmchk2 to obtain modified frcmod for both residues.
> Is it correct? Any suggestions will be appreciated.
> Thank you.
> -Tejas.
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Received on Mon Nov 06 2023 - 10:00:02 PST
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