[gmx-users] Charge fitting

2012-01-01 Thread parto haghighi 
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?)

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 0.0 1
   CB   CH3 0.0 1*
C C   0.380 2
O O  -0.380 2

[ TMP ]
 [ atoms ]
   N1NR-0.36000 0
   C2 C 0.36000 0
  NA2NT-0.83000 1
.
.
.
* CM13   CH3 0.18000 6*
  C15 C 0.18000 7
  O15OA-0.36000 7
* CM15   CH3 0.18000 7*
  C14 C 0.18000 8
  O14OA-0.36000 8
* CM14   CH3 0.18000 8*

and for atom O I have same problem:

[ ADE ]
 [ atoms ]
P P 0.99000 0
  O1POM-0.63500 0
  O2POM-0.63500 0
 * O5*OA-0.36000 0*
  C5*   CH2 0.0 1.
.
.

 * O2*OA-0.54800 8*
  H2* H 0.39800 8
  C3*   CH1   0.000 9
 * O3*OA  -0.36010*

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
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Re: [gmx-users] Charge fitting

2012-01-01 Thread 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 0.0 1
CB   CH3 0.0 1*_
 C C   0.380 2
 O O  -0.380 2

[ TMP ]
  [ atoms ]
N1NR-0.36000 0
C2 C 0.36000 0
   NA2NT-0.83000 1
.
.
.
_* CM13   CH3 0.18000 6*_
   C15 C 0.18000 7
   O15OA-0.36000 7
*_ CM15   CH3 0.18000 7_*
   C14 C 0.18000 8
   O14OA-0.36000 8
*_ CM14   CH3 0.18000 8_*

and for atom O I have same problem:

[ ADE ]
  [ atoms ]
 P P 0.99000 0
   O1POM-0.63500 0
   O2POM-0.63500 0
*_O5*OA-0.36000 0_*
   C5*   CH2 0.0 1.
.
.

*_O2*OA-0.54800 8_*
   H2* H 0.39800 8
   C3*   CH1   0.000 9
*_O3*OA  -0.36010_*

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.sehttp://folding.bmc.uu.se
--
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