Liao Chuan wrote:
Dear Gromacs users,
I obtained the ITP file of glycerol molecule from the Dundee PRODRG server
(http://davapc1.bioch.dundee.ac.uk/programs/prodrg/). However, I heard that
the charges are not accurate enough. So I estimated the charges of glycerol
using Gaussian. The input file of Gaussian is gol.gjf, including all atoms
of a glycerol molecule. The output of Gaussian is selected as follows:
-------------------------- Gaussian Output
----------------------------------------------------------------------------
-----------
Mulliken atomic charges:
1
1 O -0.677102
2 H 0.422534
3 C -0.156687
4 H 0.224462
5 H 0.169912
6 C 0.007200
7 H 0.182644
8 O -0.586768
9 H 0.435753
10 C -0.171961
11 H 0.173527
12 H 0.190745
13 O -0.630544
14 H 0.416285
Sum of Mulliken charges= 0.00000
-------------------------------------------END of Gaussian Output
----------------------------------------------------------------
------------------------------------------ ITP file
----------------------------------------------------------------------------
------
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 GOL OAB 1 -0.095 15.9994
2 HO 1 GOL HAA 1 0.043 1.0080
3 CH2 1 GOL CAA 1 0.052 14.0270
4 CH1 1 GOL CAC 2 0.078 13.0190
5 OA 1 GOL OAD 2 -0.114 15.9994
6 HO 1 GOL HAB 2 0.036 1.0080
7 CH2 1 GOL CAE 3 0.053 14.0270
8 OA 1 GOL OAF 3 -0.095 15.9994
9 HO 1 GOL HAC 3 0.042 1.0080
-------------------------------------END of ITP file
----------------------------------------------------------------------------
--
Then it comes to edit the ITP file. But there are some problems puzzling me.
Firstly, the ITP file just has 9 atoms ( see above) as the Dundee PRODRG
server uses united-atom force field which neglects 5 unpolar hydrogen atoms
while the result of Gaussian has 14 atoms. How should I edit the charges of
ITP file? Or how could I edit the cgnr and charge fields of the ITP file
with the Gaussian result? Is it reasonable and acceptable that a charge
group has a decimal number of charges?
Secondly, the charge group number of ITP file is 3 whereas the result of
Gaussian has only one charge group(14 atoms as a whole group). Could the
Gaussian package calculate the charges of a molecules by first dividing the
atoms of the molecule into different charge groups?
Any help/suggestions will be greatly appreciated!
You should read how the united-atom force field for which you are trying
to get charges worked out the charges used in their parameterization,
and do something consistent with that. Presupposing the suitability of
some other approach is likely doomed to failure.
Mark
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