[gmx-users] Charge fitting

[David van der Spoel]

On 2012-01-01 10:11, parto haghighi wrote:
> Dear GMX usesr,
>
> I have to do charge fitting for a small molecule like ethanol.
> I have applied PRODRG to generate .gro and .itp for ethanol but it has
> wrong atomic charge.
> To correct it I have to use gromos 43a1 force field parameters to assign
> charges on each atom (Is it right?)

Check this paper for gromos96 compatible stuff:
http://pubs.acs.org/doi/abs/10.1021/ct200196m

For OPLS/GAFF please check
http://virtualchemistry.org/

>
> I have red a paper ( Practical Considerations for Building
> GROMOS-Compatible Small-Molecule Topologies
> Justin A. Lemkul, William J. Allen, and David R. Bevan*) about this
> issue. In this paper they assign these value to each atom:
>
> H3C     0.000
> CH2     0.150
> O        -0.548
> H         0.398
>
> My question is:
> In a gromos 43a1 force field and in .rtp file for CH3 in ALA and TMP:
>
> [ ALA ]
>   [ atoms ]
>      N     N    -0.28000     0
>      H     H     0.28000     0
> _*CA   CH1     0.00000     1
>     CB   CH3     0.00000     1*_
>      C     C       0.380     2
>      O     O      -0.380     2
>
> [ TMP ]
>   [ atoms ]
>     N1    NR    -0.36000     0
>     C2     C     0.36000     0
>    NA2    NT    -0.83000     1
> .
> .
> .
> _* CM13   CH3     0.18000     6*_
>    C15     C     0.18000     7
>    O15    OA    -0.36000     7
> *_ CM15   CH3     0.18000     7_*
>    C14     C     0.18000     8
>    O14    OA    -0.36000     8
> *_ CM14   CH3     0.18000     8_*
>
> and for atom O I have same problem:
>
> [ ADE ]
>   [ atoms ]
>      P     P     0.99000     0
>    O1P    OM    -0.63500     0
>    O2P    OM    -0.63500     0
> *_O5*    OA    -0.36000     0_*
>    C5*   CH2     0.00000     1.
> .
> .
>
> *_O2*    OA    -0.54800     8_*
>    H2*     H     0.39800     8
>    C3*   CH1       0.000     9
> *_O3*    OA      -0.360    10_*
>
> So I am confused which one of these charges must be considered as a
> correct charge when I dont have a reference like mentioned paper?
>
> Thanks in advance.
> P.Haghighi
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se