[Open Babel] conversions

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[Open Babel] conversions

Kaitlyn Hwang
Hello!

I have two questions:

1. I get this error when converting pdb to mol2
MDL Molfile conversion failed: Molecule is too large to convert.
  File format limited to 999 atoms.
  Molecule size: 1055 atoms

Is there anything I can do to fix this or is there another
verison/software I should be using?

2. Is there a way to convert smiles to mol2?

Thanks,
kaitlyn


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Re: [Open Babel] conversions

Geoffrey Hutchison

On Nov 2, 2005, at 11:49 AM, Kaitlyn Hwang wrote:

> 1. I get this error when converting pdb to mol2
> MDL Molfile conversion failed: Molecule is too large to convert.
>   File format limited to 999 atoms.
>   Molecule size: 1055 atoms
>
> Is there anything I can do to fix this or is there another
> verison/software I should be using?

If you were converting to mol2, you would not see that error. That  
error message only comes up with the MDL .mol format, not Sybyl .mol2.

To convert from PDB to mol2, type something like this:
    babel 1ABC.pdb 1ABC.mol2

OTOH, if you're trying to convert a PDB to an MDL molfile (not mol2)  
as you said in the e-mail, you'll need to use one of the 2.0  
snapshots, which supports the v3000 Molfile and >999 atoms. (As the  
error message indicates, earlier versions of the file format do not  
support >999 atoms or bonds.)

> 2. Is there a way to convert smiles to mol2?

You can convert SMILES to mol2 easily. However, the SMILES format  
does not contain coordinates, which is probably what you're asking  
about. The current versions of Open Babel do not perform coordinate  
generation yet.

There are several ways to generate coordinates for a SMILES string.  
For example, the Gasteiger group as a webpage for their CORINA product:
http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html

Cheers,
-Geoff


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