AMBER Archive (2006)

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

From: Brian Stupi (bstupi15_at_yahoo.com)
Date: Tue Mar 07 2006 - 13:55:13 CST

The leaprc I used was leaprc.ff99

--- Brian Stupi <bstupi15_at_yahoo.com> wrote:

> 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
> templates:
> 3 Heavy
> 6 H / lone pairs
> The files contained 2 atoms not in residue
> templates
> > saveamberparm model ADENandTHYM_c_TER_mod2.prmtop
> ADENandTHYM_c_TER_c_mod2.inpcrd
> > Checking Unit.
> WARNING: There us a bond of 16.957053 angstroms
> between:
> ------- .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.
>
> Brian
>
>
> --- Thomas Cheatham <cheatham_at_chpc.utah.edu> wrote:
>
> >
> > > 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
> > 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
> > -/-
> > /-\ tec3_at_utah.edu (801) 587-9652;
> FAX:
> > (801) 585-9119
> > \-/ BPRP295A
> > http://www.chpc.utah.edu/~cheatham
> >
> >
>
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>
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