Re: AMBER: Prepin error (?) in xleap

From: Lili Peng <lilipeng.gmail.com>
Date: Thu, 30 Aug 2007 13:48:34 -0700

Hi Dr. Case,

Okay, I added the hydrogens to get the PDB file:

 REMARK Accelrys Discovery Studio PDB file

 REMARK Created: Thu Aug 30 13:40:47 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 ATOM 10 C18 GLU 1 1.933 1.409 -0.374 1.00
0.00
C ATOM 11 O20 GLU 1 2.167 0.156 -0.632 1.00
0.00
O ATOM 12 C22 GLU 1 0.785 1.600 -1.382 1.00
0.00
C ATOM 13 C23 GLU 1 -0.602 0.995 -1.094 1.00
0.00
C ATOM 14 C24 GLU 1 -1.750 1.187 -2.103 1.00
0.00
C ATOM 15 C25 GLU 1 -3.136 0.582 -1.815 1.00
0.00
C ATOM 16 O30 GLU 1 -4.020 1.377 -2.341 1.00
0.00
O ATOM 17 O32 GLU 1 -3.796 -0.414 -1.923 1.00
0.00
O ATOM 18 N34 GLU 1 -1.877 2.648 -2.420 1.00
0.00
N ATOM 19 HT GLU 1 3.887 0.681 0.280 1.00
0.00
H ATOM 20 HA GLU 1 3.642 3.359 -0.904 1.00
0.00
H ATOM 21 HB1 GLU 1 2.497 3.801 1.241 1.00
0.00
H ATOM 22 HB2 GLU 1 3.878 3.116 2.131 1.00
0.00
H ATOM 23 HG1 GLU 1 5.347 4.849 1.186 1.00
0.00
H ATOM 24 HG2 GLU 1 3.966 5.535 0.297 1.00
0.00
H ATOM 25 HC GLU 1 6.112 3.597 -0.000 1.00
0.00
H ATOM 26 1H22 GLU 1 0.642 2.675 -1.495 1.00
0.00
H ATOM 27 2H22 GLU 1 1.123 1.177 -2.328 1.00
0.00
H ATOM 28 1H23 GLU 1 -0.459 -0.079 -0.981 1.00
0.00
H ATOM 29 2H23 GLU 1 -0.940 1.419 -0.149 1.00
0.00
H ATOM 30 H24 GLU 1 -1.429 0.576 -2.946 1.00
0.00
H ATOM 31 1H34 GLU 1 -0.960 3.003 -2.843 1.00
0.00
H ATOM 32 2H34 GLU 1 -2.089 3.191 -1.522 1.00
0.00
H TER 33 GLU 1



 END






Still, when I try to run the command " antechamber -fi pdb -i glu3.pdb -fo
mol2 -o glu3.mol2" in Amber, I get the same old error message

"Warning: the assigned bond types may be wrong...

Error: cannot run "usr/local/apps/amber9/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
judgebondtype() of antechamber.c properly, exit"

I double checked the bond types of each atom, and I don't see any errors.
What am I doing wrong now? I have attached my updated PDB file for your
convenience.

Thanks,
Lili

On 8/27/07, David A. Case <case.scripps.edu> wrote:
>
> 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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>



-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Sun Sep 02 2007 - 06:07:35 PDT
Custom Search