VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
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
issue?
Thanks,
Peter

On Thu, Jun 14, 2018 at 2:27 PM, Nick Palmer <tuf90798_at_temple.edu> 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
>