[Dock-fans] error when running GRID

John Irwin jji at cgl.ucsf.edu
Thu Apr 28 22:33:09 PDT 2005


Hi -
Unsupervised, I don't think it is reasonable to expect babel or indeed any
program to convert PDB to correct mol2. The reason for this is that
chemistry is weakly defined in PDB, and so the program often must guess atom
types and bond lengths. You can use babel (or OE's molconvert.py, or sybyl,
or ...) to get into mol2 from PDB, but then you've got to look at what you
have and edit the molecule for chemistry.

Good luck!

John


John J. Irwin http://johnirwin.compbio.ucsf.edu
Adj. Assistant Professor  http://shoichetlab.compbio.ucsf.edu
Pharmaceutical Chemistry, UCSF, 600 16th St, Suite N474E
San Francisco CA 94143-2240 USA; Phone +1 415 514-4127 Fax x4260

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> -----Original Message-----
> From: dock-fans-bounces at docking.org 
> [mailto:dock-fans-bounces at docking.org] On Behalf Of Sebastien Gerega
> Sent: Wednesday, April 27, 2005 6:42 PM
> To: dock-fans at docking.org
> Subject: [Dock-fans] error when running GRID
> 
> I have a PDB file which I have converted to .mol2 using 
> Babel. When attempting to run GRID with this .mol2 file I get 
> the following error:
> 
> WARNING read_mol2: Improper ATOM record substructure id for 
> chainb.pdb in chainb.mol2.
> Error reading in receptor.
> 
> The .mol2 file starts like this:
> 
> @<TRIPOS>MOLECULE
> chainb.pdb
>  783 801 0 0 0
> SMALL
> GASTEIGER
> Energy = 0
> 
> @<TRIPOS>ATOM
>       1 N         -30.0240   -7.4760   -1.8710 N.am   24  ASN 
>     -0.1225
>       2 CA        -28.6440   -8.0580   -1.8730 C.3    24  ASN 
>      0.1785
>       3 C         -28.0090   -7.9270   -0.4840 C.2    24  ASN 
>      0.2597
>       4 O         -27.9220   -6.8240    0.0690 O.2    24  ASN 
>     -0.2718
>       5 CB        -27.7870   -7.3380   -2.9260 C.3    24  ASN 
>      0.1169
> 
> Can anyone see anything wrong with this? Or give me more 
> insight into what the problem is?
> thanks,
> Sebastien Gerega
> 
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