Missing bond in chloroform .rtp files
There is a problem with the CHCL3 directive in all Gromos96 .rtp files. None of them define a bond between C and H. For ffG43a1, ffG43a2, and ffG45a3, the correct line should read:
CChl HChl gb_36
For ffG53a5 and ffG53a6, the correct line should be:
CChl HChl gb_39
As well, the atom names given in the .rtp entry are impossible to satisfy in a .pdb file, given the fact that the chlorine atoms are five characters long. I would suggest they be changed to, i.e., CL1, CL2, and CL3. I have implemented this setup in my own files without issue.
#1 Updated by Berk Hess about 10 years ago
There is no missing bond here.
All solvent models in GROMOS, including chloroform, are completely rigid.
All bonds should be constrained. Adding the bond, and thus constraint,
you suggest result in an more constraints than DOF's, which should be avoided.
The atom naming is unfortunate, but I don't think we should adapt the atom
names to the most restrictive format.