Re: [OpenBabel-Devel] obminimize

[<chr...@bt...>]

Hi,

I'm not sure why pdb was the output format I was certainly not expecting it.
On 19 Nov 2010, at 13:55, Pascal Muller wrote:

> Hi,
> 
>> MASTER        0    0    0    0    0    0    0    0   16    0   16    0
>> END
>> ENDMDL
>> MODEL        3
>> COMPND    UNNAMED
>> AUTHOR    GENERATED BY OPEN BABEL 2.3.0
> 
> I don't know if it will help, but the tag "END" should be the very
> last line of the PDB file. There is only one occurence of "END" per
> pdb file.
> http://www.wwpdb.org/documentation/format23/sect11.html
> 
> And ENDMDL is at the end of each model.
> http://www.wwpdb.org/documentation/format23/sect9.html
> 
> And I think that the COMPND and AUTHOR records are not allowed within
> the MODEL record - but won't matter that much, I think :)
> 
> Normally, it's the same molecule / same author for each model, only
> the coordinates are modified.
> 
> But could have e.g. (see http://www.wwpdb.org/documentation/format23/sect2.html)
> COMPND    MOL_ID: 1;
> COMPND   2 HEMOGLOBIN;
> COMPND    MOL_ID: 2;
> COMPND   2 BENZENE
> like in many PDB complex.
> 
> Btw, compound name is lost when converting, with babel 2.2.3, .pdb to
> .smi or .sdf.
> 
> But I never use pdb format as multi-mol file, and I always convert my
> protein-ligand pdb complex in mol2... :)
> Never used obminimize too.
> 
> Regards,
> Pascal