[Dock-fans] error when running GRID

John Irwin jji at cgl.ucsf.edu
Thu Apr 28 22:37:01 PDT 2005


Ooops, I replied too quickly to this one. Conversion programs generally do
fine on pure protein PDB files. It is on small molecules where they have to
guess chemistry. You need a substructure record for the grid program. Good
luck. John


John J. Irwin http://johnirwin.compbio.ucsf.edu
Adj. Assistant Professor  http://shoichetlab.compbio.ucsf.edu
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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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