[AMBER] Question about ff14SB parameters/atom types for TYR

From: Dr. Anselm Horn <anselm.horn.fau.de>
Date: Tue, 8 Jun 2021 11:56:36 +0200

Dear all,

while trying to create ff14SB parameters for a tyrosine derivative, I
came across something in the parameter files I do not understand:

In the ff14SB publication (Maier et al. 2015) referenced in the Amber21
manual, it is reported that new atom types are introduced and used when
needed; for TYR, Supplement Tables S1 and S2 list chi torsional angles
that comprise two new atom types, namely CX and 2C.

While I find the atom type CX for the TYR carbon alpha atom in the
ff14SB parameter files, I cannot find 2C for the carbon beta, despite
its description in the paper.

Since I intend to stay as close as possible to the original ff14SB TYR
parameters for my TYR-derivative, I'm not sure which the actual ff14SB
parameters are for TYR - maybe I missed something completely.
Thus, any clarification is greatly appreciated!

I used AmberTools version 21.03, and Amber version 20.11.
Starting from leaprc.protein.ff14SB, I inspected the parameter files
loaded there, parm10.dat and frcmod.ff14SB; the later holds the
definition of the 2C atom type and the corresponding parameters.
The actual residue description resides in amino12.lib, which lacks a 2C
atom type for TYR (using CT for carbon beta instead), but contains 2C
atom types for other standard residues (ASN, ASP, CYS, GLN, GLU, ILE,
LEU, MET, SER). BTW, the situation seems similar for PHE.
For carbon beta of other amino acids with ring systems (HIS and TRP),
however, the force field library files and the paper description do
agree: CT is used for carbon beta.

I'm looking forward to hints from the experts!

Best regards,


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Received on Tue Jun 08 2021 - 03:00:02 PDT
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