AMBER Archive (2004)

Subject: AMBER: Add Hydrogen bond through xLeap?

From: Nan Lin (
Date: Wed Jun 02 2004 - 01:25:18 CDT

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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