AMBER Archive (2009)

Subject: Re: [AMBER] Problem with loading PDB into tleap

From: Kamali Sripathi (
Date: Wed Aug 19 2009 - 09:06:15 CDT

Thanks for your reply, Ashish!

I'm sorry; I forgot to mention that I'm working with a PDB of RNA. I guess
I'm just confused because I don't put the hydrogens in, leap does when I try
to load the pdb file into leap. I've tried just deleting them and loading
again, but it gives me the same error message. Even more strangely, these
protons only occur after the O3' of the guanosine residues.

Thanks again!


On Wed, Aug 19, 2009 at 9:56 AM, Ashish Runthala

> hello Kamali,
> You need to remove these protons to stabilize the protein confirmation.
> Any normal amino acid start from nitrogen (N) and end on CG or CD
> groups, indicating the proper link of peptide bond with the next
> residue, but the erroneous protons are
> there after this CG or CD atoms, which needs to be removed.
> For your simplicity, remember that the following atoms are generally
> present as the erroneous protons after the CG or CD atoms, before the
> N atom of the next residue starts in the PDB file.So remove these
> entries from pdb file. Look at these atoms.
> All these are erroneous. Generally, such protons are marked as
> H, 1H,2H,3H, HA,HB,HC, HG1,HG2,HD1,HD2, 1HB, & 2HB.
> Remove such entries and protonate using leap, if you wish before doing
> further steps.
> Ashish
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