AMBER Archive (2008)

Subject: AMBER: unable to open pdb file

From: Taufik Al-Sarraj (
Date: Wed Dec 03 2008 - 20:44:09 CST


I am unable to open a pdb file in molmol, the error message is
unknown residues: DA, DC, DG, DT, HIE, Na+
unknown atoms: OXT (ARG+), OXT (GLU), H1, H2, H3 (LYS+), H1, H2, H3 (MET)

I started with a pdb file from the protein data bank, i ran a
minimization and then i used ambpdb to create a pdb file from *.rst
file. I would like to compare the initial pdb file to the pdb file after

> ambpdb -p *.prmtop < *.rst> *.pdb

i tried -aatm option and protonate -d $AMBERHOME/dat/PROTON_INFO.Brook
-i old.pdb new.pdb

is there another way to create a pdb file?

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