Re: [AMBER] tLeap adding non-library hydrogens

From: Huang Jing <>
Date: Wed, 4 Jan 2017 12:16:38 +0200

Put all the coordinate including hydrogen atoms for non-library residues in
pdb file, and then it could no errors,

On Wed, Jan 4, 2017 at 12:07 PM, David Poole <> wrote:

> Okay, here is a fun one.
> 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.
> In all three of these cases, extra hydrogens are added, in the case of
> 'no hydrogens' starting point, there are also numerous missing
> hydrogens.
> I've had tleap also write out the element from the mol2, and it works fine.
> The names of the hydrogens added by any method 'should be' the same.
> I am not sure what to do, this rather frustrating to say the least. I
> am running AmberTools15, so maybe would this have been fixed with any
> changes to 16? I will test it today as well.
> -D
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Received on Wed Jan 04 2017 - 02:30:04 PST
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