Hi All, Following is the structure of the molecule, which I wish to parameterize. CH3 O | || CH3 - C - O - C - | CH3 It is a peptide capping reagent. The last carbon will form bond with the NH2 group of the peptide. I have generated the the topology using PRODRG server and wish to refine the charge group and partial charges as PRODRG server doen't predict them correctly. The closest well-validated structure is of carboxyl ester in the first position of DPPC (or any other glyceride). However there is a minor difference. The carbon attached to three methyl group, in this case is CH0 type and in DPPC it was CH2 type. Since the carbon was part of charge group in DPPC, I fear I may have to change the partial charges. I couldn't find any example where exactly same charge group was used. I will appreciate if anyone can suggest me how to assign correct partial charges.
Thanks a lot for the help. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.