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

Thomas Schlesier schlesi at uni-mainz.de
Fri Sep 11 11:54:31 CEST 2009

Gaussian03 (don't know which version you use) gives also the charges for
united atoms (all hydrogen-charges put into the heavy atoms). So look in
the output file (.out) under your posted charges.
But be aware that the GROMACS force field weren't parametrized with QM
calculations (so you must persuade the community that this way of
parametrization is ok).
I think a better way would be to look after the atomtypes of the force
field and use this charges (ok, we have a alcohol group -> looking in
ff*nb.itp we find an alcohol O atom and then we use that parameters ...).
This way i think you will be nearer to the original force field as if
you use QM charges.



Message: 3
Date: Thu, 10 Sep 2009 22:55:12 +0800
From: "Liao Chuan" <liaochuan at tju.edu.cn>
Subject: [gmx-users] How to edit the cgnr and charge fields of a ITP
	file	with the result of Gaussian?
To: <gmx-users at gromacs.org>
Message-ID: <001a01ca3226$b2cb1480$0300a8c0 at ERIC>
Content-Type: text/plain; charset="us-ascii"

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  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

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