Dear Users,
I have used the parmchk2 to generate frcmod file of
azobenzene which is connected to cysteine residue.
My frcmod file is given below
=================================
Remark line goes here
MASS
N 14.010 0.530 same as n
H 1.008 0.161 same as hn
H1 1.008 0.135 same as h1
S 32.060 2.900 same as ss
c3 12.010 0.878
hc 1.008 0.135
c2 12.010 0.360
n 14.010 0.530
ca 12.010 0.360
nf 14.010 0.530
ne 14.010 0.530
ha 1.008 0.135
o 16.000 0.434
h1 1.008 0.135
C 12.010 0.616 same as c
O 16.000 0.434 same as o
BOND
H -N 403.20 1.013 same as hn- n, penalty score= 0.0
-----------------------
------------------------
ANGLE
H1-CX-N 0.000 0.000 ATTN, need revision
----------------------
--------------------------
DIHE
H1-2C-CX-N 2 1.400 0.000 3.000
S -2C-CX-N 1 0.469 0.000 1.000
O -C -CX-N 1 0.000 0.000 0.000
H1-CX-N -H 1 0.000 0.000 0.000
2C-CX-N -H 1 0.000 0.000 0.000
C -CX-N -H 1 0.000 0.000 0.000
--------------------------
----------------------------
IMPROPER
c3-n -c2-o 1.1 180.0 2.0 Using the
default value
c2-c2-n -ca 1.1 180.0 2.0 Using the
default value
ca-ca-ca-n 1.1 180.0 2.0 Using the
default value
ca-ca-ca-ha 1.1 180.0 2.0 Using general
improper torsional angle X- X-ca-ha, penalty score= 6.0)
ca-ca-ca-nf 1.1 180.0 2.0 Using the
default value
ca-ca-ca-ne 1.1 180.0 2.0 Using the
default value
NONBON
N 1.8240 0.1700 same as n
H 0.6000 0.0157 same as hn
CX 0.0000 0.0000 ATTN, need revision
H1 1.3870 0.0157 same as h1
-----------------------
---------------------------
========================================
The parameters for improper dihedrals are not present in parm10.dat and
gaff.dat files.
How parmchk2 is filling these values in frcmod file?
----------------------
Please help me in fixing this issue.
Thanks
MD
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Received on Tue Mar 05 2019 - 09:30:02 PST
