[gmx-users] Re: CT3 terminal

[Pär Bjelkmar]

Hello,

> I use pdb2gmx command to convert a pdb file to a .gro and .top file(using
> CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3.
> When I use editconf to get a pdbfile from the .gro file generated, the C=0
> and the NCH3  seem to clash in space in pymol.
> 
> Is there a way of correcting this?

this sounds fishy, might be an error in the formation of the CT3. Have to look into that. What GROMACS version are you running?

/Pär Bjelkmar