AMBER Archive (2006)Subject: AMBER: The plc.frcmod file in the old version tutorial

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Nov 12 2006 - 20:50:29 CST

Dear all,

In the old version of the Amber tutorial, there is the
following plc.frcmod:

---------------
plc.frcmod

# modifications to force field for poplar
plastocyanin

MASS
CU 65.36

BOND
NB-CU 70.000 2.05000 #kludge by JRS
CU-S 70.000 2.10000 #kludge by JRS
CU-SH 70.000 2.90000 #for pcy
CT-SH 222.000 1.81000 #met(aa)

ANGLE
CU-NB-CV 50.000 126.700 #JRS estimate
CU-NB-CR 50.000 126.700 #JRS estimate
CU-NB-CP 50.000 126.700 #JRS estimate
CU-NB-CC 50.000 126.700 #JRS estimate
CU-SH-CT 50.000 120.000 #JRS estimate
CU-S -CT 50.000 120.000 #JRS estimate
CU-S -C2 50.000 120.000 #JRS estimate
CU-S -C3 50.000 120.000 #JRS estimate
NB-CU-NB 10.000 110.000 #dac estimate
NB-CU-SH 10.000 110.000 #dac estimate
NB-CU-S 10.000 110.000 #dac estimate
SH-CU-S 10.000 110.000 #dac estimate
CU-SH-CT 50.000 120.000 #JRS estimate
CT-CT-SH 50.000 114.700 #met(aa)
HC-CT-SH 35.000 109.500
H1-CT-SH 35.000 109.500
CT-SH-CT 62.000 98.900 #MET(OL)

DIHE
X -NB-CU-X 1 0.000 180.000 3.000
X -CU-SH-X 1 0.000 180.000 3.000
X -CU-S -X 1 0.000 180.000 3.000
X -CT-SH-X 3 1.000 0.000 3.000

NONBON
CU 2.20 0.200
-----------------

There is something I do not understanding:

1.
BOND
NB-CU 70.000 2.05000 #kludge by JRS

What is the meaning of 70.000? And what is the meaning
of 2.05000?

2.
ANGLE
CU-NB-CV 50.000 126.700 #JRS estimate
Does CU-NB-CV means the bond formed by CU, NB,CV with
CU and CV at each side of NB?

What is the meaning of 50.000? And what is the meaning
of 126.700?

3.

DIHE
X -NB-CU-X 1 0.000 180.000 3.000
What will be the definition of X? What is the
definition of -NB-CU-X? What is the meaning of
1,0.000, 180.000,3.000 separately?

4.
NONBON
CU 2.20 0.200
I think NONBON should mean nonbounded, then what is
the definition of 2.20 and 0.200 separately?

Best regards.

Fenghui Fan

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