Hello Sorry if I address an already covered issue. I happened to notice that adding up the ffamber03 partial charges for ARG doesnt yield +1 but ~1.6. Also, for CYX the total charge is ~0.87. Is this is a known issue?
In the .itp file, pdb2gmx adds up rounded charge values (as seen in the qtot column) and so the total ARG charge comes up to +1 and for CYX 0. In .tpr, i.e. in the simulation, the full charge values are used, as they are contained in the ffamber03.rtp but grompp doesn issu warnings for non-integer total charge save for rounding errors. Thanks in advance. George Dr. George Patargias Polymer IRC Group University of Leeds Leeds, LS2 9JT, UK _______________________________________________ gmx-users mailing list [email protected] http://www.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
