[gmx-users] question: atoms with charges in zwetter ions

[Mark Abraham]

Sven Huttenhouse 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?

I expect gmx2pdb would ignore the charge column in the PDB file. Use 
pdb2gmx -inter and make some sensible choices. Basically, the PDB format 
is too limited to reliably express all the information you'd want for a 
molecule, which is why pdb2gmx outputs a topology file too.

Mark