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

From: Brian Stupi <>
Date: Tue, 7 Mar 2006 11:30:59 -0800 (PST)

Amber community,

Here is the error message I received (that was not
included in the original email):

> model = loadpdb “ADENandTHYM_c_TER_c_mod2.pdb”
Load PDB files: ./ADENandTHYM_c_TER_c_mod2.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<01P 2>
   Added missing heavy atom: .R<DT 8>.A<02P 3>
   Total atoms in file: 248
   Leap added 9 missing atoms according to residue
          3 Heavy
          6 H / lone pairs
   The files contained 2 atoms not in residue
> saveamberparm model ADENandTHYM_c_TER_mod2.prmtop
> Checking Unit.
WARNING: There us a bond of 16.957053 angstroms
------- .R<DA 7>.A<03’ 32> and .R<DT 8>.A<P 1>
WARNING: The unperturbed charge of the unit: -7.000000
is not zero.
FATAL: Atom .R<DT5 4>.A<A 31> does not have a type.
FATAL: Atom .R<DT 8>.A<A 33> does not have a type.
Failed to generate parameters
Parameter file not saved.

The program I am using is tleap (xleap will not work
on the terminal I use). I also tried to insert the
"TER" to the PDB file but when I save the text file as
a PDB in Chimera, it does appear in the PDB file. I
also tried using just the Text file but received
similiar error messages. I will try the suggestions
Thomas stated below.

Thank you for your time and help in advance.


--- Thomas Cheatham <> wrote:

> > I am trying to transfer my PDB file for an 8 base
> > 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
> leaprc.ff94):
> 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
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

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Received on Sun Mar 12 2006 - 06:10:13 PST
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