On Mon, Aug 27, 2007, Lili Peng wrote:
>
> Thanks for your reply. I tried running antechamber initially (as you
> prescribed), but my converted mol2 file is really weird. The carbon atoms
> get converted to Californium and Cerium atoms. There's even a Neon atom in
> the structure, as well as many "Unknowns". I have no idea how the carbon
> atoms got converted into them.
Here is the "glu3.pdb" file:
REMARK Accelrys Discovery Studio PDB file
REMARK Created: Mon Aug 27 13:56:43 Pacific Daylight Time 2007
ATOM 1 N GLU 1 3.326 1.548 -0.000 1.00 0.00 N
ATOM 2 CA GLU 1 3.970 2.846 -0.000 1.00 0.00 C
ATOM 3 CB GLU 1 3.577 3.654 1.232 1.00 0.00 C
ATOM 4 CG GLU 1 4.267 4.996 1.195 1.00 0.00 C
ATOM 5 CD GLU 1 3.874 5.805 2.429 1.00 0.00 C
ATOM 6 OE1 GLU 1 4.595 5.679 3.454 1.00 0.00 O
ATOM 7 OE2 GLU 1 2.856 6.542 2.334 1.00 0.00 O
ATOM 8 C GLU 1 5.486 2.705 -0.000 1.00 0.00 C
ATOM 9 O GLU 1 6.009 1.593 -0.000 1.00 0.00 O
TER 10 GLU 1
HETATM 11 C A 1 -1.198 -0.215 0.736 1.00 0.00 C
HETATM 12 C A 1 0.108 0.559 0.560 1.00 0.00 C
HETATM 13 C A 1 1.275 -0.423 0.476 1.00 0.00 C
HETATM 14 C A 1 2.565 0.342 0.301 1.00 0.00 C
HETATM 15 O A 1 3.623 -0.259 0.212 1.00 0.00 O
HETATM 16 N A 1 -1.398 -1.128 -0.431 1.00 0.00 N
HETATM 17 C A 1 -2.351 0.756 0.820 1.00 0.00 C
HETATM 18 O A 1 -3.054 0.784 1.816 1.00 0.00 O
HETATM 19 O A 1 -2.590 1.543 -0.148 1.00 0.00 O
TER 20 A 1
END
Antechamber is limited in the types of pdb files it can handle:
1. Every atom in a residue needs to have a unique atom name. You have five
atoms all named "C". (Actually, antechamber takes care of this, but other
parts of amber will not, so it is a good idea to make sure of it by hand.)
2. The input pdb file must have all atoms present, *including hydrogens.*
This is where you really go wrong, since there are no hydrogen atoms present
in your input file. See if discovery studio can put these on, or build them
by hand in xleap, or in some other modeling program.
3. The things you think are Californium, neon, etc, are really atom types,
not elements. Given that it had no hydrogens, antechamber tried to make
multiple bonds between lots of things, and the quantum optimization was of
course very weird.
So: edit the names in the pdb file, and get some hydrogens on there!
...good luck...dac
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Received on Wed Aug 29 2007 - 06:07:29 PDT
