AMBER Archive (2006)

Subject: Re: AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Fri Aug 11 2006 - 08:57:46 CDT

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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