Re: [AMBER] Amber parmeters for ACE-CYX bond

From: Ali Saad Kusay <akus8786.uni.sydney.edu.au>
Date: Mon, 23 Aug 2021 10:50:03 +0000

Hi Carlos,

Thanks very much for this, rarely does this level of detail make into publications

I did eventually make a prmtop file by using a custom ACE residue with one less hydrogen and bonding it to CYX through the sulphur atom. I generated an angle from the GAFF2 library and between ACE: C-CT|-|S :CYX which is missing from the protein forcefield.

The issue was that the dihedrals across the ACE-CYX interface looked weird and this was not helped by simply generating these particular dihedrals using GAFF2. The angles in question are ACE: N-C-C|-|S :CYX and ACE: C-C|-|S-C :CYX and when I compared the ones produced by Antechamber and a QM dihedral scan, there was significant difference between them.

What I ended up doing is using the Lipargen server to generate OPLS parameters, for C-S-C-C it identified that this is similar to the methionine side chain and for N-C-C-S, that it is similar to this series of atoms in cysteine and assigned dihedrals accordingly.

This was a good learning experience for me so thanks again for your help

Cheers,

Ali Kusay

´╗┐On 5/8/21, 10:22 pm, "Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:

    you probably would want to create a new residue that corresponds to the
    modified ACE without one hydrogen. WHen you fit parameters for it (such as
    partial charges), it's probably best to choose a model compound that has a
    sulfur attached to the carbon, or perhaps an attached CYX depending on your
    resources. the bond itself could be added in leap as one would do with a
    disulfide.
    We did a similar procedure for a cofactor bound to a CYX using GAFF and
    antechamber, and the methods description might serve as an example:
    https://pubs.acs.org/doi/full/10.1021/acschembio.0c00543

    On Wed, Aug 4, 2021 at 1:00 AM Ali Kusay <Ali.Kusay.anu.edu.au> wrote:

> 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
>
>
>
>
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Received on Mon Aug 23 2021 - 04:00:02 PDT
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