AMBER Archive (2006)

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

From: Brian Stupi (
Date: Tue Mar 07 2006 - 13:30:59 CST

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

Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to