Hi,
When I use Open Babel to transfer a pdb file to a mol2 file, there is no
> @<TRIPOS>SUBSTRUCTURE tag in the output file. My question is exactly the
> same as Yuri Pevzner's one
> <http://sourceforge.net/p/openbabel/mailman/message/27101046/>. However,
> the thread was stopped after Pascal Muller's reply.
>
> To answer his questions:
>
>> What kind of substructure info, coming from the pdb file, do you need in the
>> mol2?
>>
>> I want to make a mol2 file of a ligand (AB1) of the 1RV7.pdb (it's a
> HIV-1 protease). I extracted it by using grep AB1 1RV7.pdb > AB1.pdb.
>
You don't need the @<TRIPOS>SUBSTRUCTURE tag for conversion into mol2, as
far as I know.
But keeping the CONNECT table, if present, for the ligand (no occurrence of
the ligand identifier in these lines...), is better.
Anyway, conversion from pdb in mol2 is not reliable enough for ligands
(bonds type are not explicit and often wrong in the mol2 output).
What about editing yourself the pdb structure, correct bond type, and
saving in mo2? But I would go for downloading the ligand file :)
http://www.pdb.org/pdb/explore/explore.do?structureId=1RV7
http://www.pdb.org/pdb/download/downloadLigandFiles.do?ligandIdList=AB1&structIdList=1RV7&instanceType=all&excludeUnobserved=false&includeHydrogens=false
This sdf could be converted in mol2.
>
> Also, I would like to add H atoms to have them appear in mol2 output, with
> AMBER99 force field. Do you have any suggestion for this?
>
obabel option -h
Regards,
Pascal
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