Hi,
I am working on some prmtop files of small druglike-molecules. The prmtop
files are prepared by Antechamber-1.26. In some cases, I noticed that some
LENNARD_JONES_ACOEF and BCOEF are zero. For example, in the particular case,
there are 9 zero entries in both coefficients (entry 2, 3, 5, 8, 12, 17, 23,
30, 38). By further analysis, I found that all those zero entries are
corresponding to the interactions between a particular atom type (oh) and
any other atom types. Does it mean that the program does not have parameters
for oh or the Lennard-Jones interaction between this atom type and other
atoms are neglected by purpose? Thank you.
Regards,
Jing
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
5.81803229E+05 0.00000000E+00 0.00000000E+00 7.91544157E+05
0.00000000E+00
1.04308023E+06 4.66922514E+04 0.00000000E+00 6.78771368E+04
3.25969625E+03
6.82786631E+04 0.00000000E+00 9.71708117E+04 4.98586848E+03
7.51607703E+03
7.44975864E+05 0.00000000E+00 9.95480466E+05 6.20665997E+04
8.96776989E+04
9.44293233E+05 7.01803794E+05 0.00000000E+00 9.24822270E+05
6.01816484E+04
8.61541883E+04 8.82619071E+05 8.19971662E+05 4.71003287E+05
0.00000000E+00
6.47841731E+05 3.69471530E+04 5.44261042E+04 6.06829342E+05
5.74393458E+05
3.79876399E+05 6.00750218E+04 0.00000000E+00 8.59947003E+04
4.33325458E+03
6.55825601E+03 7.91627154E+04 7.62451550E+04 4.77908183E+04
5.71629601E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
6.99746810E+02 0.00000000E+00 0.00000000E+00 6.93079947E+02
0.00000000E+00
6.75612247E+02 1.03606917E+02 0.00000000E+00 1.06076943E+02
1.43076527E+01
1.25287818E+02 0.00000000E+00 1.26919150E+02 1.76949863E+01
2.17257828E+01
7.50714425E+02 0.00000000E+00 7.36907417E+02 1.13252061E+02
1.36131731E+02
8.01323529E+02 6.14502845E+02 0.00000000E+00 5.99015525E+02
9.40505980E+01
1.12529845E+02 6.53361429E+02 5.31102864E+02 6.29300710E+02
0.00000000E+00
6.26720080E+02 9.21192136E+01 1.11805549E+02 6.77220874E+02
5.55666448E+02
5.64885984E+02 1.16187983E+02 0.00000000E+00 1.18043746E+02
1.63092814E+01
2.00642027E+01 1.26451907E+02 1.04660679E+02 1.03580945E+02
1.85196588E+01
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 29 37
2
3 5 8 12 17 23 30 38 4
5
6 9 13 18 24 31 39 7 8
9
10 14 19 25 32 40 11 12 13
14
15 20 26 33 41 16 17 18 19
20
21 27 34 42 22 23 24 25 26
27
28 35 43 29 30 31 32 33 34
35
36 44 37 38 39 40 41 42 43
44
45
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
oh ho c3 h1 h1 c3 hc hc c3 hc hc c3 hc hc c3 h1 h1 n c
o
n c3 cx cx cx hc hc hc hc hc h1 h1 c3 c3 ca ca ca ca ca
ca
ha ha ha ha ha hc hc h1 c3 oh ho h1 c3 oh ho h1 c3 h1 c3
hc
hc ca ca ha ca ha ca ha ca ha ca ha
- All opinions expressed in this message are not necessarily those of
VeraChem LLC.
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Received on Sun Aug 13 2006 - 06:07:12 PDT
