[gmx-users] OPLS group charges
Erik Lindahl
lindahl at csb.stanford.edu
Wed Nov 5 19:50:01 CET 2003
Hi,
No - the OPLS charges are calculated from QM, and not tuned to give
neutral charge groups. The current setup is a compromise between two
things:
1. It is nice to have charge groups since it speeds up
neighborsearching and reduces problems from cut-offs
2. Very large charge groups (the whole aminoacid would normally be
neutral) can give very bad errors since the cut-off distance is based
on the group-group center distance.
Btw, if you use PME you don't need charge groups - it is just a way to
speed up neighborsearching in that case.
Cheers,
Erik
On Nov 5, 2003, at 9:57 AM, Germana Paterlini wrote:
> In skimming through the OPLS charges, I noticed that some amino acids
> do not have a "charge = 0"
> in each charge group. Some backbone atoms charges are also grouped
> differently.
> The effect of these is probably minor, since the total charge is
> correct. Are these just typos?
>
>
> Thanks,
> Germana Paterlini
>
>
>
> Two examples below
>
> [ ARG ]
>
> [ atoms ]
>
> N opls_238 -0.500 1
>
> H opls_241 0.300 1
>
> CA opls_224B 0.140 1
>
> HA opls_140 0.060 1
>
> CB opls_136 -0.120 2
>
> HB1 opls_140 0.060 2
>
> HB2 opls_140 0.060 2
>
> CG opls_308 -0.050 3
>
> HG1 opls_140 0.060 3
>
> HG2 opls_140 0.060 3
>
> CD opls_307 0.190 4
>
> HD1 opls_140 0.060 4
>
> HD2 opls_140 0.060 4
>
> NE opls_303 -0.700 4
>
> HE opls_304 0.440 4
>
> CZ opls_302 0.640 4
>
> NH1 opls_300 -0.800 4
>
> HH11 opls_301 0.460 4
>
> HH12 opls_301 0.460 4
>
> NH2 opls_300 -0.800 4
>
> HH21 opls_301 0.460 4
>
> HH22 opls_301 0.460 4
>
> C opls_235 0.500 5
>
> [ ASN ]
>
> [ atoms ]
>
> N opls_238 -0.500 0
>
> H opls_241 0.300 0
>
> CA opls_224B 0.140 1
>
> HA opls_140 0.060 1
>
> CB opls_136 -0.120 2
>
> HB1 opls_140 0.060 2
>
> HB2 opls_140 0.060 2
>
> CG opls_235 0.500 3
>
> OD1 opls_236 -0.500 3
>
> ND2 opls_237 -0.760 4
>
> HD21 opls_240 0.380 4
>
> HD22 opls_240 0.380 4
>
> C opls_235 0.500 5
>
> O opls_236 -0.500 5
>
>
>
>
>
>
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