[gmx-users] How to edit the cgnr and charge fields of a ITP file with the result of Gaussian?

[Liao Chuan]

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!

 

Thank you!!

Chuan Liao

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090910/624063e0/attachment.html>