VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Tue Nov 30 2021 - 21:52:27 CST

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>
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!oePUWhHhANH6OoK4NmCH2kogJPmmz1KOHdzypO8PKmDE0EP1n3kO01EzYjamrJHvvA$ ),
> 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
>>
>>