VMD-L Mailing List

From: Hideyuki Miyatake (miyatake_at_riken.jp)
Date: Mon Dec 06 2021 - 04:30:50 CST


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<mailto: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<mailto: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