[gmx-users] question

[Andrew Bostick]

Dear Justin,

For 2 new entries in aminoacids.rtp file, I deleted OE2 atom of GLU
residue and HZ2 and HZ3 atoms of LYS residue. Is it true? I compared
CYS and CYS2 residues in aminoacids.rtp file, in both case all atoms
exist (unlike my case). But there are difference in charges and charge
groups. How to set charges and charge groups in my case (for Gly2 and
Lys2)?


You mentioned to special bond distance matrix. Which file contains special
bond distance matrix, after pdb2gmx?