Hi Jing,
Are you sure that's oh (oxygen atom of hydroxy group), not ho (hydrogen
atom of hydroxy group)? oh should have acoef and bcoef, but ho doesn't.
Guanglei
Jing Huang wrote:
> 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 - 06:07:13 PDT
