Re: [AMBER] Antechamber prep question

From: <gilbert.bluemarble.net>
Date: Fri, 10 Jul 2009 14:10:32 +0100

Quoting FyD <fyd.q4md-forcefieldtools.org>:

> Dear Andrew,
>
> > I have perused the archives and found similar topics but i still
> > cant figure this out.  I have a ligand that was docked using
> > Autodock and im now attempting to insert into the receptor to run
> > some MD on it.  So im trying to correct the atom types and charges
> > using antechamber.  I am following the basic tutorial on antechamber
> > so im attempting to convert my pdb to mol2 but i get this error
> > that alot of people are getting;
> > [pcp]:Research/AMBER/ATP] NAME% $AMBERHOME/bin/antechamber -i
> > atp_H_1.pdb -fi pdb -o ATP.mol2 -fo mol2 -c bcc
> > For atom[7]:O5, the best APS is not zero, bonds involved by this
> > atom are frozen
> > The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> > (aromatic double)Error: cannot run
> > "/usr/local/Amber10/amber10/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > judgebondtype() of antechamber.c properly, exit
> > I add H's everywhere and charges (Not sure if that is necessary)
> > using chimera and run the same command and i get;
> > 4 is not a valid atom id in CONECT    4   22    5    2   40
>
> If you look at http://archive.ambermd.org/200812/0329.html, we can
> provide you many cofactors for different FF versions (& not only ATP).
> The charges and FF libraries were built using a global
> procedure//building block approach in a single R.E.D. job, and not
> each factor taken individually.
> For instance it was possible to build AMP, ADP, ATP, AQP and more
> generally XYP, X = (d)A, (d)C, G, (d)T & (d)Y, = M, D, T, etc... and
> even more.
>
> regards, Francois
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>


Dear Andrew,

  I looked at your atp_h...pdb file with several graphics programs it and looks
like your problems start with the addition of the hydrogen atoms. I don't know
if your original pdb file started with ATP - where the atoms would have been
entered as ATOMS with a residue of A - but most PDB readers use a library of
connectivities for known structures so that the user does not need to add the
connectivity to the file. When you enter atoms as HETATM then the library can
not be used the the program needs to determine the connectivity of the structure
by other means - usually distance tests - and may not be able to get the correct
connectivity. If you don't have the correct connectivity then you won't get the
correct hydrogen atom addition. You can get around this by adding connect
statements to your pdb file. The other approach is to read the pdb file into a
graphical editor and add/delete the bonds as necessary. Your structure has
hydrogen atoms on each of the ring nitrogens and neither Pcmodel or Chimera are
able to correctly determine the connectivity from your PDB file. Reading your
pdb file into chimera and saving it as a mol2 file shows the problems in
assigning connectivity. I suggest you go back to the original PDB file, read it
with Chimera, save it as a mol2 file without the hydrogens and then (if you
don't have a graphical editor) edit the connectivity by hand until it is
correct. Then you should be able to correctly add the hydrogens and proceed.

regards

Kevin

Kevin E. Gilbert
Serena Software



Received on Fri Jul 10 2009 - 10:09:33 PDT
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