AMBER Archive (2005)

Subject: AMBER: Tyrosine CZ Parameterization Bug continues in Amber 8

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Thu Sep 01 2005 - 17:04:21 CDT

A bug documented on the reflector in 2003 does not seem to have been fixed in
Amber 8

When you source leaprc.ff99 from leap, these commands are processed:

#
# Load the main parameter set.
#
parm99 = loadamberparams parm99.dat
...
#
# Load main chain and terminating
# amino acid libraries.
#
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib

While parm99.dat has correct torsion terms:

X -CA-OH-X 2 1.80 180.0 2. Junmei et al, 99
X -C -OH-X 2 4.60 180.0 2. Junmei et al, 1999

the all_amino*94.lib files have Tyrosine still parameterized as type C instead
of CA. Thus, tyrosine is too rigid under simulation.

This was better explained by others back in 2003:

http://structbio.vanderbilt.edu/archives/amber-archive/2003/1113.php

I'm rementioning it because it might impact simulation results, and it really
should be fixed.

I can understand reluectance to change the parm*.dat and the all_amino*.lib
files, as "fixing" them in one place might botch their user in other
combinations. But, the leaprc.ff99 appears to definitely give a "bad" result.
Perhaps TYR should just be redefined in that file, going forward.

Thanks
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