[gmx-users] question: atoms with charges in zwetter ions
anoddlad at yahoo.com
Fri Nov 4 20:58:13 CET 2005
Use the pdb2gmx option -inter to specify charges. I'm
not sure if this will translate back into a .pdb
output, but it definitely works within gromacs.
--- Sven Huttenhouse <mdsimulation at hotmail.com> wrote:
> Dear all
> I'm trying to get a pdb file for Glycine in
> solution. Glycine form a
> zwetter-ion in water, it has a positive charge on
> the Nitrogen atom and a
> negative charge on the single bond oxygen atom.
> I've generated a .pdb file with these specifications
> (I assigned the charges
> on columns 79 and 80 according to the pdb format).
> However I tried to use
> this file with pdb2gmx to get a .pdb file again and
> I got a file without
> charges at the atoms.
> How can I let gromacs recognise the charges on the
> atoms in such a molecule?
> kind regards
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