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.
Greetings Thomas ------------------------------ Message: 3 Date: Thu, 10 Sep 2009 22:55:12 +0800 From: "Liao Chuan" <[email protected]> Subject: [gmx-users] How to edit the cgnr and charge fields of a ITP file with the result of Gaussian? To: <[email protected]> Message-ID: <001a01ca3226$b2cb1480$0300a...@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 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 _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
