[gmx-users] (no subject)

[Zhili Zuo]

hello all:
I want to generate the topology for the ligand. But my ligand is composed of eight residues, six of them are GLU, LEU, ASP, VAL, GLU and PHe, and two of them are non-peptide residues in the middle.
when I made top file in www.davapc1.bioch.dundee.ac.uk, the hydrogens in all the carboxyl were missing and the coordinate of hydrogen to the nitrogen in the last GLU  is "nan".

How can I generate the proper topology of my ligand?
Thank you!!