Hello,
I was checking the VDW parameters, and got some questions.
For Amber ff14SB, the VDW parameters are stored in parm10.dat and
frcmod.ff14SB.
Here are some lines from the beginning of parm10.dat:
C 12.01 0.616 ! sp2 C carbonyl group
CA 12.01 0.360 sp2 C pure aromatic (benzene)
CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring
junction
CC 12.01 0.360 sp2 aromatic C, 5 memb. ring HIS
CD 12.01 0.360 sp2 C atom in the middle of: C=CD-CD=C
I understand that the first column is atom type, the second is mass, but
I don't understand the third column.
And I also found that the third column is not in parm94.dat. Does it
mean that the third column is not important?
I then found the VDW parameters for some atom type at the end of parm10.dat
#
N NA N2 N* NC NB NT NY
C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ CP CS
MOD4 RE
H 0.6000 0.0157 !Ferguson base pair geom.
HO 0.0000 0.0000 OPLS Jorgensen,
JACS,110,(1988),1657
HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
HC 1.4870 0.0157 OPLS
H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
H2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
#
I don't understand the two lines of listing all the atom types of carbon
and nitrogen, and I did not find many of those VDW parameters.
Where are those VDW parameters? What is the meaning of "MOD4 RE" ?
Could someone give me some tips on my questions? Thanks a lot!
All the best,
Qinghua
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Received on Fri Jan 25 2019 - 03:30:02 PST
