Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations

From: Thomas Cheatham <>
Date: Mon, 6 Mar 2006 16:51:08 -0700 (Mountain Standard Time)

> I am trying to transfer my PDB file for an 8 base DNA
> Duplex and make the Amber *.prmtop and *.inpcrd files.
> I am getting the messages below.

I do not see any message, and from the information given it is very
difficult to figure out what is wrong without actually trying it myself,
which I did...

By "transfer", do you mean using the loadPdb command in LEaP?

> I have inserted a TER line to separate the strands.

This is good and necessary so that 5' and 3' terminals are properly
recognized. Assuming you are loading up LEaP, what leaprc file was used?
If you are using leaprc.ff94 or leaprc.ff99 (both appropriate for nucleic
acids), in those files you can see pdbResMap's that morph from the
standard residue to names to AMBER nucleic acid names, i.e. "ADE" to
"DA5", "DA ", and "DA3" depending on its location (which necesitates
addition of that TER card between strands).

In addition, those leaprc files change the * names to ' names, i.e. O5* -> O5'.

I notice that your PDB file has HETATM records instead of ATOM records,
but LEaP has no trouble with this.

I loaded up the first PDB into LEaP and received the following (using

 bb = loadpdb amber1.pdb
Loading PDB file: ./amber1.pdb
Created a new atom named: H within residue: .R<DT5 4>
Created a new atom named: H within residue: .R<DT 8>
  Added missing heavy atom: .R<DT 8>.A<P 1>
  Added missing heavy atom: .R<DT 8>.A<O1P 2>
  Added missing heavy atom: .R<DT 8>.A<O2P 3>
  total atoms in file: 248
  Leap added 9 missing atoms according to residue templates:
       3 Heavy
       6 H / lone pairs
  The file contained 2 atoms not in residue templates

Adding missing atoms errors are usually benign if the atom was indeed
missing (and not already "created" as a new atom name). However, in this
case it is funny because we do not expect terminal phosphates. Looking at
the PDB file supplied, there is no TER card between residues 7 and 14 in
that PDB (as numbered). That error will not prevent prmtop formation, but
it is not correct without the TER card...

The "Create a new atom named" warnings are more insidious, as an atom is
added, but not found in the residue templates. This will be fatal. Looking
at those atoms named "H", they should be H5T. Either delete the two
terminal H atoms, rename them to H5T or alter the pdb name map to morph H
into H5T in residues DT5.

The second PDB file is not completely in PDB format so will choke LEaP.
You will need unique atom names and supply residue names. If this is a
drug like molecule, you are advised to look at Antechamber and GAFF to
build up the necessary files...

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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Received on Sun Mar 12 2006 - 06:10:10 PST
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