Re: [AMBER] Generating a HETATM database to use with reduce

From: Kucharski Jr., Amir N <>
Date: Fri, 15 Jul 2016 01:04:54 +0000

Thank you for your response.

What commands do I need to use in tleap in order to do this? I know how to load the mol2 and pdb files, but what is the command to save a new pdb file with the proper hydrogen configurations?


From: David A Case <>
Sent: Thursday, July 14, 2016 8:51:23 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Generating a HETATM database to use with reduce

On Thu, Jul 14, 2016, Kucharski Jr., Amir N wrote:
> I am trying to do simulations on several protein-ligand complexes. I
> know from the SUS tutorial that reducing the ligand to add hydrogens
> is a key early step, but these ligands do not have entries in the
> database that reduce uses. To remedy this, we have tried making our
> own database from connectivity information in the mol2 files. We have
> followed the input format for the default library, but when we direct
> reduce to our database using the -DB tag, still no hydrogens are
> added. Is there another file we would need to make? Any help is much
> appreciated. Thanks!

What you describe should work, and you might have to put debugging information
into the reduce code to see why it is not doing what you expect.

However: if you already have a mol2 file with hydrogens, you can use tleap
to add hydrogens, bypassing the reduce step. Just load the mol2 file,
and a pdb file (missing hydrogens), and the output pdb file will have the
hydrogens added in their canonical positions.

...good luck...dac

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