From: Nick Palmer (
Date: Wed Jun 20 2018 - 12:38:12 CDT

Hello Peter,

I did actually find the atoms, they were moved and not missing, in the
generated pdb file, their coordinates were set to 0 for an unknown reason.

As for the procedure, I took the residue I was trying to edit from a larger
pdb file, the mCherry protein residue 65 and 66, and pasted them into a new
pdb file. I then manually added hydrogens into the file where they were
expected to be. Upon completion of adding the hydrogens I saved the file as
a pdb file and then loaded it up into vmd. The new pdb had moved carbon
atoms. I fixed this by adding the hydrogens from this file to the original
file and it worked fine.

Let me know if you need more information.

On Fri, Jun 15, 2018 at 1:27 PM, Peter Freddolino <>

> 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 <> 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

Nicholas J. Palmer