[gmx-users] Re: CT3 terminal
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:
> > 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
> > When I use editconf to get a pdbfile from the .gro file generated, the
> > 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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