[AMBER] questions on VDW parameters

From: Qinghua Liao <scorpio.liao.gmail.com>
Date: Fri, 25 Jan 2019 12:06:02 +0100


I was checking the VDW parameters, and got some questions.

For Amber ff14SB, the VDW parameters are stored in parm10.dat and

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
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,
   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,

AMBER mailing list
Received on Fri Jan 25 2019 - 03:30:02 PST
Custom Search