On Thu, Feb 08, 2024, Noureen Abdelrahman via AMBER wrote:
>
>I am trying to parametrize a non-standard residue (biliverdin) covalently
>bound to a cysteine residue.
First advice, if you have not already done so: see what others have done
along these lines. The search term "biliverdin molecular dynamics" yields
a number of hits, not all using Amber. But this one does:
https://pubs.acs.org/doi/full/10.1021/jp301456j
N.B. I just did a quick search here. You are in a better postion to judge
which papers are most likely to help.
>I am following the Amber tutorial: Simulating
>the Green Fluorescent Protein and Building a Modified Amino Acid Residue. I
>downloaded the .ciff file for the JRA ligand from PDB, produced the .ac
>file using antechamber, and my .mc file looks like this:
>
>Could not find bond parameter for atom types: S - CM
>Could not find angle parameter for atom types: S - CM - CM
>Could not find angle parameter for atom types: S - CM - CT
>Could not find angle parameter for atom types: 2C - S - CM
> ** No torsion terms for atom types: 2C-S-CM-CM
> ** No torsion terms for atom types: 2C-S-CM-CT
You need to add these parameters to some frcmod file that you load into
tleap. There is not "automated" way to create such covalent linkages. Here
is one approach:
create a small molecule with a CH3-CH2-S group (representing the cysteine
side chain) and a biliverdin molecule, with an S-C bond. You might be able
to get a pretty good starting structure by taking coordinates from the PDB
file you have.
run antechamber to get its (GAFF) parameters.
copy the paramters you need into your new frcmod file, changing the atom
types (by hand), converting GAFF types to Amber types.
...good luck...dac
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Received on Sun Feb 11 2024 - 12:00:02 PST
