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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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