[gmx-users] Re: CT3 terminal

Sai Pooja saipooja at gmail.com
Tue Oct 26 14:37:23 CEST 2010

GROMACS 4.5 with charmm.

So one solution could be to open the output pdb file in a software like
Pymol, correct the coordinates and then make changes in the .gro file? Or do
I also need to edit the other files?


On Tue, Oct 26, 2010 at 1:29 AM, Pär Bjelkmar <bjelkmar at cbr.su.se> wrote:

> 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--
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