X-C-CN-X is not present in amber03 in the GROMACS distribution. You seem to be using some modified version. Please ask the person who modified it :-)
Mark On Wed, Apr 24, 2013 at 4:26 PM, Elisa Frezza <elisa.fre...@gmail.com>wrote: > Dear All, > > I am starting to use amber03 force field, but I have found something very > strange for proper angle dihedral. > > On the basis of definition of proper dihedral function in AMBER and GROMACS > manual I aspect that the following conversion from amber to gromacs: > > k_n(GROMACS)=4.18/2 V_n (AMBER) > > where n= multiplicity. > > If I compare ffbonded.itp file in ffamber03 folder and the parameter > reported in amber I find something very strange and I do not understand > what it is right: > > constant angle > multiplicity > AMBER: X C CN X 8.00 180 2 > GROMACS X C CN X 16.736 180 2 > # kn= 4.18/2 V_n > > constant angle > multiplicity > AMBER: X C NA X 5.648 180 > 2 > GROMACS X C NA X 5.648 180 2 > # kn= 4.18/4 V_n > > the ratios between kn and Vn are different. > Have someone some suggestions or explanation? > > Thanks in advance > > Elisa > > -- > Elisa Frezza > Ph.D. Student in Materials Science and Engineering > Dipartimento di Scienze Chimiche > Università di Padova > via Marzolo, 1 > 35131 Padova - Italy > Phone: +39 049 827 5149 > Skype: elisa.frezza > Emai: elisa.fre...@gmail.com > elisa.fre...@studenti.unipd.it > > > > > > -- > Elisa Frezza > Ph.D. Student in Materials Science and Engineering > Dipartimento di Scienze Chimiche > Università di Padova > via Marzolo, 1 > 35131 Padova - Italy > Phone: +39 049 827 5149 > Skype: elisa.frezza > Emai: elisa.fre...@gmail.com > elisa.fre...@studenti.unipd.it > -- > 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
