VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Tue Nov 30 2021 - 21:45:06 CST

Hi Miyatake,

On a purely technical level, I think your issue is likely involving the
bond section of your parameter file. If you look over the existing amino
acids, their topology files all have the following bond present: 'BOND C
+N'. This defines a bond between the carboxyl carbon and the next amino
acid in the chain's nitrogen backbone atom. Without it, your peptide will
terminate after your non-canonical amino acid. If it's terminating before
your residue, that's likely because the atom name 'N' doesn't exist in your
residue - if your backbone nitrogen atom's name is 'N1' or similar, it
won't work.

That ties into what's likely to be a larger issue here - the backbone atoms
won't be the correct atom types either, given it's generated purely using
CgenFF. There's likely going to be more work required than just generating
the file with CGenFF and inserting it into your peptide - to ensure the
peptide behaves correctly, you'll need to make sure that your amino acid's
backbone has the correct partial charges and atom types for the standard
CHARMM36 force field. There's a FAQ entry explaining how to appropriately
generate bonds between CGenFF and the standard CHARMM FF available (
https://urldefense.com/v3/__https://mackerell.umaryland.edu/*kenno/cgenff/faq.php*hybrid__;fiM!!DZ3fjg!uMGYjCA3luvN5dhH1Co2_UbXmsloRRNFIIrZARa9ilLovwAJSQlMUkNZG6nN4doNvw$ ), but given
the similarities of L-DOPA and Tyrosine, it will likely be more appropriate
(and easier) to develop a patch for the TYR amino acid to generate L-DOPA,
rather than parameterise a full amino acid.

Regards,
Michael Robinson

On Wed, 1 Dec 2021 at 14:08, Hideyuki Miyatake <miyatake_at_riken.jp> wrote:

> Hello,
>
> I want to incorporate L-DOPA (DAH) residues into proteins.
>
> I generated DAH.str by CGEN-FF for QwikMD, but the L-DOPA residues
> were disconnected with other natural residues.
>
> How can I have the L-DOPA residues connected with other residues?
>
> Miyatake
>
>