From: Enrico Martinez (
Date: Wed Sep 07 2022 - 08:53:25 CDT

right, thank you!
In fact the module reduce of ambertools could not add protons to a
particular ligand in a proper way, this is why I was looking for
another solution

Il giorno mer 7 set 2022 alle ore 14:53 Peter Freddolino
<> ha scritto:
> Hi Enrico,
> If you are preparing for MD simulations, then presumably you have topology files for use by psfgen or *leap? These should specify the protonation states that you actually want to simulate anyway right? Since both of those pieces of software can also add the protons I don't understand the need for the extra step.
> Best,
> Peter
> On Wed, Sep 7, 2022 at 3:45 AM Enrico Martinez <> wrote:
>> Thank you very much Peter!
>> Actually I need to protonate a small molecule prior to the MD
>> simulation with Amber and NAMD. In some cases molefacture predicts
>> protonation much better compared to the openbabel, so I need to
>> integrate it to my scripting pipeline to produce protonated input. BTW
>> if no-gui mode is not possible, may I open quickly in the terminal vmd
>> gui-session which will open on the fly the Molefacture window in vmd
>> with my small molecule ?? ;-)
>> Cheers
>> Enrico
>> Il giorno mar 6 set 2022 alle ore 23:42 Peter Freddolino
>> <> ha scritto:
>> >
>> > Hi Enrico,
>> > What is the intended downstream application for the modified file? Molefacture is pretty tightly wrapped up with the GUI, so this is not going to be easy to pull off. You can see the set of steps that it uses in the ::Molefacture::add_all_hydrogen function in molefacture_builder.tcl, but I am not sure whether the state will update properly without the GUI running. (Perhaps someone who has worked on molefacture more recently than me can provide an estimate. It definitely would have crashed and burned last I tried). This package is really intended for interactive usage. Using babel/openbabel (general case) or psfgen (if you're planning to use the resulting molecules for MD simulations with NAMD) is almost certainly going to be easier.
>> > Best,
>> > Peter
>> >
>> > On Tue, Sep 6, 2022 at 6:03 AM Enrico Martinez <> wrote:
>> >>
>> >> Dear VMD users!
>> >> I need to protonate a small molecule using the Molefacture plugin. I
>> >> have already done it via VMD gui and now would like to test batch mode
>> >> that should be activated using:
>> >> vmd -dispdev text -e input.file |& output.file
>> >>
>> >> Could you please suggest to me a possibility of the script which will
>> >> call Molefacture from the script for such purpose?
>> >> Many thanks in advance
>> >> Enrico
>> >>