Hi Eric Thanks for your reply. You are right, the charges in my ffamber03.rtp add up to +1 too. I got the ffamber 2003 ports for gmx331 from the site you mentioned. Actually, it was my mistake. When I transcribed the charges from the ffamber03.rtp to another file I missed the minus sign from the N atom...I'm sorry about that. Thanks again George
________________________________ Από: [EMAIL PROTECTED] εκ μέρους Eric J. Sorin Αποστολή: Σαβ 5/10/2008 12:48 πμ Προς: gmx-users@gromacs.org Θέμα: Re: [gmx-users] Non integer charge for ARG and CYX? Hi George, I just quickly checked the partial charges in ARG from the GROMACS v3.3.1 ffamber03.rtp file and the charges due indeed sum to +1, so I'm not sure why you're seeing non-integer total charge in the .rtp file .... it sounds like you might have a file that was modified by someone and maybe you need to update your ffamber files (?). Please tell me: Did you get these files from http://chemistry.csulb.edu/ffamber/? Which version of GROMACS are you using? Which set of ffamber ports (shown in the top of the .rtp file)? Thanks! Eric ----- Original Message ----- From: "Georgios Patargias" < > To: <gmx-users@gromacs.org> Sent: Thursday, May 08, 2008 4:09 AM Subject: [gmx-users] Non integer charge for ARG and CYX? 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 gmx-users@gromacs.org 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
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