[gmx-users] from n2t to topology with similar groups

[Claire M.]

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