Jason,
Thank you for the explanation. When I first load the pdb file into tleap,
I get the following output:
......
Created a new atom named: H485 within residue: .R<TA1 844>
Created a new atom named: H487 within residue: .R<TA1 844>
Created a new atom named: H489 within residue: .R<TA1 844>
Created a new atom named: H491 within residue: .R<TA1 844>
Created a new atom named: H493 within residue: .R<TA1 844>
Created a new atom named: H495 within residue: .R<TA1 844>
Created a new atom named: H497 within residue: .R<TA1 844>
Created a new atom named: H499 within residue: .R<TA1 844>
Created a new atom named: H501 within residue: .R<TA1 844>
Created a new atom named: H503 within residue: .R<TA1 844>
Created a new atom named: H505 within residue: .R<TA1 844>
Created a new atom named: H507 within residue: .R<TA1 844>
Created a new atom named: H509 within residue: .R<TA1 844>
Created a new atom named: H511 within residue: .R<TA1 844>
Created a new atom named: H513 within residue: .R<TA1 844>
Created a new atom named: H515 within residue: .R<TA1 844>
Created a new atom named: H517 within residue: .R<TA1 844>
Created a new atom named: H519 within residue: .R<TA1 844>
Created a new atom named: H521 within residue: .R<TA1 844>
Created a new atom named: H523 within residue: .R<TA1 844>
total atoms in file: 13333
Leap added 1864 missing atoms according to residue templates:
2 Heavy
1799 H / lone pairs
63 unknown element
The file contained 2238 atoms not in residue templates
I then try to save the amber parameter files and I get the following output:
...
FATAL: Atom .R<TA1 844>.A<H465 229> does not have a type.
FATAL: Atom .R<TA1 844>.A<H467 230> does not have a type.
FATAL: Atom .R<TA1 844>.A<H469 231> does not have a type.
FATAL: Atom .R<TA1 844>.A<H471 232> does not have a type.
FATAL: Atom .R<TA1 844>.A<H473 233> does not have a type.
FATAL: Atom .R<TA1 844>.A<H475 234> does not have a type.
FATAL: Atom .R<TA1 844>.A<H477 235> does not have a type.
FATAL: Atom .R<TA1 844>.A<H479 236> does not have a type.
FATAL: Atom .R<TA1 844>.A<H481 237> does not have a type.
FATAL: Atom .R<TA1 844>.A<H483 238> does not have a type.
FATAL: Atom .R<TA1 844>.A<H485 239> does not have a type.
FATAL: Atom .R<TA1 844>.A<H487 240> does not have a type.
FATAL: Atom .R<TA1 844>.A<H489 241> does not have a type.
FATAL: Atom .R<TA1 844>.A<H491 242> does not have a type.
FATAL: Atom .R<TA1 844>.A<H493 243> does not have a type.
FATAL: Atom .R<TA1 844>.A<H495 244> does not have a type.
FATAL: Atom .R<TA1 844>.A<H497 245> does not have a type.
FATAL: Atom .R<TA1 844>.A<H499 246> does not have a type.
FATAL: Atom .R<TA1 844>.A<H501 247> does not have a type.
FATAL: Atom .R<TA1 844>.A<H503 248> does not have a type.
FATAL: Atom .R<TA1 844>.A<H505 249> does not have a type.
FATAL: Atom .R<TA1 844>.A<H507 250> does not have a type.
FATAL: Atom .R<TA1 844>.A<H509 251> does not have a type.
FATAL: Atom .R<TA1 844>.A<H511 252> does not have a type.
FATAL: Atom .R<TA1 844>.A<H513 253> does not have a type.
FATAL: Atom .R<TA1 844>.A<H515 254> does not have a type.
FATAL: Atom .R<TA1 844>.A<H517 255> does not have a type.
FATAL: Atom .R<TA1 844>.A<H519 256> does not have a type.
FATAL: Atom .R<TA1 844>.A<H521 257> does not have a type.
FATAL: Atom .R<TA1 844>.A<H523 258> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I'm guessing that I'm getting these errors because of the 63 "unknown
elements" and the "atoms not in residue templates" when I loaded the pdb
file. Is this just from Accelyrs, or is it because there was some other
error in the file?
Thanks,
Matt
On Sat, Oct 29, 2011 at 6:03 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hi Matt,
>
> Antechamber is designed to derive charges for a small ligand that docks in
> a protein, not an entire protein. It runs a semi-empirical quantum
> mechanical calculation to determine the charge density around the molecule,
> and then fits partial charges to match that electrostatic potential, more
> or less. QM calculations are quite expensive, and they're never run on
> full proteins to determine charges. They're run on small compounds and
> single amino acid/nucleic acid residues to define charges for that residue,
> which are then used on full proteins. As the error message suggests,
> antechamber will not work for full proteins, as that's not what it was
> designed for.
>
> My guess is that Accelrys messed up some of the atom and/or residue naming
> in your PDB which prevents leap from recognizing your structure. The only
> time you should need to run antechamber (or get other parameters) is when
> you have non-standard amino acids or other small organic molecules in your
> structure. All other residues (standard amino acids and nucleic acid
> residues) should have their parameters already defined in existing
> parameter sets (including parameters and partial charges).
>
> If you print out the full error you're getting on the first step, we may be
> able to help more.
>
> HTH,
> Jason
>
> On Sat, Oct 29, 2011 at 5:51 PM, Matthew D Antalek
> <mantale1.binghamton.edu>wrote:
>
> > Hi all,
> >
> > I modified the 1JFF structure from pdb.org using Acclerys, and saved
> the
> > structure as a pdb file. I then loaded the file into leap and tried to
> > generate the prmtop and inpcrd file but i was getting "FATAL" errors when
> I
> > tried to save. So I figured it was because there were some parameters
> > missing or LEaP wasn't recognizing some of the atoms. Then I tried to
> > follow
> > the steps on this tutorial to try and use antechamber to fix the pdb
> file,
> > but I got more errors.
> >
> >
> > Warning: detected more than 10 Residue sequence numbers;
> > this may be a large multiple residue PDB file;
> > large multiple residue PDB files are not supported.
> > Continuing, but problems may be encountered.
> > The atom number exceeds the MAXATOM, reallocate memory
> > Info: the bond number exceeds MAXBOND, reallocate memory automatically
> >
> > Error: cannot run "/home/matthew/amber11/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > judgebondtype() of antechamber.c properly, exit
> > [matthew.matt-pc octMD]$
> >
> >
> > I got the initial "warning" message many many times. If anyone knows if
> > there is something that must be done for large pdb files or if anyone
> knows
> > of a good antechamber tutorial, please let me know.
> >
> > Sincerely,
> > Matt Antalek
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Oct 29 2011 - 15:30:03 PDT
