AMBER Archive (2009)

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

From: Ashish Runthala (
Date: Wed Aug 19 2009 - 08:56:59 CDT

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.


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