Re: [AMBER] Fixing pdb files prepared in VMD, minor errors

From: David A Case <>
Date: Mon, 1 Jul 2013 21:44:57 -0400

On Mon, Jul 01, 2013, Hunter Brown wrote:

> So I had recently e-mailed about a problem I had. Most of the errors
> were caused by the histidine residue being named 'HSD' instead of 'HIS'
> (which I changed in the PDB file. This left 72 errors (down from 450ish,
> not bad).
> The 72 errors all say something like: atom CD does not have a type, atom
> OT1 does not have a type, atom OT2 does not have a type.
> The problem atoms were CD, OT1, and OT2.
> All of the problem atoms were on the ILE and VAL residues, with the
> exception of 2 on the CVAL residue (if I am not mistaken, CVAL is not a
> standard residue name, what should I change the name to?).

Just compare the atom names in the PDB file you got from VMD (or wherever)
versus those in a "real" PDB file that you download from

CHARMM has used the wrong name for the c-delta of ILE since the beginning
of time, and also uses OT1,OT2 instead of O,OXT for the terminal
carboxylate group at the end of the chain.

CVAL just means: C-terminal valine. Change this to VAL (although I'm a little
surprised that CVAL didn't work.)

Another approach is to ask people on the CHARMM or VMD support sites what
tools they use to create PDB files with correct atom and residue names.


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Received on Mon Jul 01 2013 - 19:00:03 PDT
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