Hi, No, you should never change the charges in a force field!
Run pdb2gmx again with the -nochargegrp option. That will make the size of all charge groups a single atom. This will be done automatically in the 4.5.2 release which will be out soon. Berk Date: Fri, 17 Sep 2010 02:32:31 -0700 From: meetnah...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] ARG Charmm gmx 4.5.1 Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13 CT2 1 ARG CD 4 0.2 12.011 ; qtot 1.2 14 HA 1 ARG HD1 4 0.09 1.008 ; qtot 1.29 15 HA 1 ARG HD2 4 0.09 1.008 ; qtot 1.38 16 NC2 1 ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1 ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1 ARG CZ 4 0.64 12.011 ; qtot 1.76 19 NC2 1 ARG NH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1 ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1 ARG HH12 4 0.46 1.008 ; qtot 1.88 22 NC2 1 ARG NH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1 ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1 ARG HH22 4 0.46 1.008 ; qtot 2 to Message body CD 0.18 HD1 0.06 HD2 0.06 NE -0.7 HE 0.4 CZ 0.6 NH1 -0.8 HH11 0.5 HH12 0.5 NH2 -0.8 HH21 0.5 HH22 0.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists