AMBER Archive (2003)

Subject: I still have problems with parm99.dat

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Wed May 21 2003 - 08:37:19 CDT

Dear Amber users,

I still have some problems to understand the file parm99.dat.
At the end of the torsions, there are some torsions for which IDIVF are
not determined :

X -X -C -O 10.5 180. 2.
JCC,7,(1986),230
X -O2-C -O2 10.5 180. 2.
JCC,7,(1986),230
X -X -N -H 1.0 180. 2.
JCC,7,(1986),230
X -X -N2-H 1.0 180. 2.
JCC,7,(1986),230
X -X -NA-H 1.0 180. 2.
JCC,7,(1986),230
X -N2-CA-N2 10.5 180. 2.
JCC,7,(1986),230
X -CT-N -CT 1.0 180. 2.
JCC,7,(1986),230
X -X -CA-HA 1.1 180. 2. bsd.on C6H6
nmodes
X -X -CW-H4 1.1 180. 2.
X -X -CR-H5 1.1 180. 2.
X -X -CV-H4 1.1 180. 2.
X -X -CQ-H5 1.1 180. 2.
X -X -CK-H5 1.1 180. 2.
X -X -CM-H4 1.1 180. 2.
X -X -CM-HA 1.1 180. 2.
X -X -CA-H4 1.1 180. 2. bsd.on C6H6
nmodes
X -X -CA-H5 1.1 180. 2. bsd.on C6H6
nmodes
CK-CB-N*-CT 1.0 180. 2.
CM-C -N*-CT 1.0 180. 2. dac guess,
9/94
CM-C -CM-CT 1.1 180. 2.
CT-O -C -OH 10.5 180. 2.
NA-CV-CC-CT 1.1 180. 2.
NB-CW-CC-CT 1.1 180. 2.
NA-CW-CC-CT 1.1 180. 2.
CW-CB-C*-CT 1.1 180. 2.
CA-CA-CA-CT 1.1 180. 2.
C -CM-CM-CT 1.1 180. 2. dac guess,
9/94
NC-CM-CA-N2 1.1 180. 2. dac guess,
9/94
CB-NC-CA-N2 1.1 180. 2. dac, 10/94
NA-NC-CA-N2 1.1 180. 2. dac, 10/94
CA-CA-C -OH 1.1 180. 2. (not used in
tyr!)
CA-CA-CA-OH 1.1 180. 2. in tyr
H5-O -C -OH 1.1 180. 2. Junmei et
al.1999
H5-O -C -OS 1.1 180. 2.
CM-CT-CM-HA 1.1 180. 2. Junmei et
al.1999
CA-CA-CA-Br 1.1 180. 2. Junmei et
al.1999
CM-H4-C -O 1.1 180. 2. Junmei et
al.1999
C -CT-N -H 1.1 180. 2. Junmei et
al.1999
C -CT-N -O 1.1 180. 2. Junmei et
al.1999

What does this mean ? Are these torsion parameters used by Amber ? And
if so, how
can I know which IDIVF is associated with each torsion ?

Tahnks a lot for your answers,
Fabien 

--
__________________________________________________________________
Fabien Cailliez                         Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique      e-mail : cailliez_at_ibpc.fr
IBPC    13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________