VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Mon Dec 06 2021 - 05:41:07 CST

Hi Miyatake,

The angle between CT2, C, and NG3P3 is going to be between atomtypes
belonging to the CHARMM36 forcefield (CT2, C) and the CGenFF force field
(NG3P3). These have the same parametrization philosophy and so work well
for non-bonded interactions, but no parameters exist for bonded
interactions between these two force fields. L-DOPA might have existing
parameters available, I've not looked, but if you can't find them, a
program like FFParam would allow you to fairly easily optimize the
parameters to ensure it's appropriate for your molecule.

Regards,
Michael Robinson

On Mon, 6 Dec 2021 at 22:28, Hideyuki Miyatake <miyatake_at_riken.jp> wrote:

>
> Even after I added the parameters in my .str file,
> It did not fix.
>
> Does anyone kindly give me the example files of L-DOPA containing pdb file
> and the corresponding DAH.str file?
>
> No matter what I tried, I could not fix the problem by myself.
>
> Miyatake
>
>
> 2021/12/06 3:42、Georcki Ropon <groponp_at_gmail.com>のメール:
>
> Add CGenFF parameters and check if it fix your problem.
>
>
> Geo.
>
> On Dec 4, 2021, at 07:00, Hideyuki Miyatake <miyatake_at_riken.jp> wrote:
>
> Hello,
>
> I’m trying to incorporate L-DOPA in my protein.
>
> First, I mutated a TYR to L-DOPA and generated DAH.str by CGenFF for
> QwikMD run.
>
> However, it stopped with comments like
>
> “FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 C NG3P3 (ATOMS 22
> 25 27)”
>
> Or something like that. I cannot fix the missing information.
>
> Please someone tell me what the best way to solve this kind of problem,
> e.g. incorporation of
> non-natural amino acids in proteins.
>
> Thank you.
>
> Miyatake
>
>
>
>