VMD-L Mailing List

From: Hideyuki Miyatake (miyatake_at_riken.jp)
Date: Tue Nov 30 2021 - 21:59:13 CST

Dear Michael,

Thank you so much for your kind suggestions.

             Miyatake

2021/12/01 12:52、Michael Robinson <michael.robinson1_at_monash.edu<mailto:michael.robinson1_at_monash.edu>>のメール:

Quick correction - my first sentence said 'involving the bond section of your parameter file' when it should actually say ' involving the bond section of your topology file' - but given CgenFF outputs these together as a toppar file, I'd imagine you'd find it regardless!

On Wed, 1 Dec 2021 at 14:45, Michael Robinson <michael.robinson1_at_monash.edu<mailto:michael.robinson1_at_monash.edu>> wrote:
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!sB5ek-IjIDXNaz3-neZigXWrHY7l3Jp90QYt4JtbwIPFb_C47eY__P_pyXl0euNkoQ$ ), 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<mailto: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