Dear All, I am trying to generate the topology file of a structure of highly substituted GO sheets via n2t-file. I have written a n2t-file accounting for every group present in the structure. With the charges I have set for each atom, I should get a neutral structure, but I don’t. I’ve managed to understand that the problem lies in some atoms like the O atoms and the H atoms of -oh and -cooh groups, being too similar in the coordinate file. When building the topology, GROMACS assigns all O and H to the fist atomtype present in the n2t-file. I’ve thought I could force the position of the similar atoms, in order to obtain differences of distance, via VMD and then re-write the n2t. It would require a massive amount of time, so I beg you all for better ideas before I start.
Thanks you a lot for getting there, hope to hear you soon, Claire -- 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.
