From: Peter Freddolino (
Date: Thu Jan 28 2016 - 00:00:28 CST

Hi Sho,
This really depends on what you want to do with the structures afterwards. If you’re going to use them for any kind of simulation, you’re probably best off using the toolchain appropriate for system preparation for your simulations (e.g., psfgen for namd). If you really just want to add the proton and do nothing else, you can call molefacture from the scripting interface too, but it is not for the faint of heart. You’d need to do
package require molefacture
to load it up, and then call ::Molefacture::molefacture_gui_aux to initialize the molecule and ::Molefacture::add_hydrogen (both with appropriate arguments — the source code is at least somewhat decently documented in these portions) to add the hydrogen, and then save the resulting structure.
There are also easier ways, depending on some details of your problem; for example, you could write your own script that adds two hydrogens to a pdb file, and then opens up vmd and moves them to appropriate places. But we could provide more useful help if you gave more details on what you’re going to use the files for.


> On Jan 27, 2016, at 11:15 AM, Shoresh Shafei <> wrote:
> Hi,
> I have 200 pruned pdb files in which I would like to add a hydrogen to atom A and one to atom B. I know that for a pdb file, this can be done using molefacture, however I wonder if there is a script to automate this process for 200 pdb files.
> Best
> Sho