From: Peter Freddolino (
Date: Fri Jun 15 2018 - 12:27:16 CDT

Hi Nick,
Joshua's recent post gives you the practical answer, but I'm
concerned/surprised by the missing atoms in your pdb written by
molefacture. Can you give me an exact procedure to try reproducing this

On Thu, Jun 14, 2018 at 2:27 PM, Nick Palmer <> wrote:

> Hello everyone, I am making a topology file for the chromophore in the
> mCherry protein and I I need to add hydrogens to the molecule in order to
> get IC values in a table. I have tried using molefacture, however every
> time I add the hydrogens to the molecule and write it to a pdb, several
> carbon atoms end up missing from the file. I have also tried getting the IC
> values from the xbgf file generated from the molefacture, but it doesn't
> generate anything I can really use. Is there an easier way to do this that
> I am not aware of?
> --
> Nicholas J. Palmer