Re: [AMBER] tLeap adding non-library hydrogens

From: David Case <>
Date: Wed, 4 Jan 2017 08:20:47 -0500

On Wed, Jan 04, 2017, David Poole wrote:
> I'm putting together a model in tleap, I have a mol2 file with the
> correct structure and a series of PDB files that contain multiple
> copies of the 'residue' defined by the mol2 file.
> These files either have the crystal hydrogens, no hydrogens, or
> hydrogens added by Chimera.

I assume by "these files" you mean the pdb files. Each one should be run
through pdb4amber before being sent to tleap. (Indeed, almost all user files
should go through pdb4amber first.) Use the --nohyd option to remove existing
hydrogens, and let tleap add them back in using the information in the mol2

> In all three of these cases, extra hydrogens are added, in the case of
> 'no hydrogens' starting point, there are also numerous missing
> hydrogens.

Are there missing hydrogens in the mol2 file? If so, you'll have to fix that.
"Extra" hydrogens are probably being added because the hydrogen names in the
PDB files don't match the hydrogen names in the mol2 file.

I'm guessing a lot here, since you only gave a rather vague description of the
problem. If pdb4amber doesn't help, you'll have to post files for an example.

Another debugging strategy: use the desc command in tleap to examine the
residue that is loaded via your mol2 file. Make sure tleap has found all the
atoms and hydrogens that you expect to be there.


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Received on Wed Jan 04 2017 - 05:30:05 PST
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