AMBER Archive (2004)

Subject: Re: AMBER: Add Hydrogen bond through xLeap?

From: Guanglei Cui (
Date: Wed Jun 02 2004 - 09:06:47 CDT


What you try to do is probably only adding hydrogen atoms, not hydrogen
bonds? I guess what happened is you have some non-amino acid or
nucleotide residue in your system, and xleap/tleap doesn't know the
correct atom types for those atoms. To do this correctly in xleap,
you'll need to assing atom types, either manually or with antechamber.
Babel does quite a good job in adding hydrogen atoms ... I've tried it
with a few ligands with double bonds. Hope this helps.


Nan Lin wrote:

> Hi,
> I am new to Amber and I am trying to run MD simulation for a
> protein-ligand complex downloaded from PDB bank. I have run the
> following commands through xLeap trying to add hydrogen bonds to the
> ligand( there are no hydrogens for the ligand in the downloaded pdb file)
> >xleap -f leaprc.ff99
> >com = loadpdb com.pdb # after this the atom are not connected at all
> >bondbydistance com # atoms are connected, but several bond
> orders are wrong
> >Util/Add H bond & Build
> But I found several bond orders for ligand are wrong, for example double
> bond has been changed to the single bond. So hydrogens are also added wrong.
> Please help if anyone know how to resolve this problem. Thanks in advance.
> Nan Lin
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