On 23 Jan 2012, at 12:29, Douglas Houston wrote:
> Hi all,
>
> I wonder if anyone can help me work out what's going on here. I'm trying to
> convert a PDB file of ADP (from structure 3ATV) to mol2 format and add
> hydrogens. The first step seems to work fine:
>
> babel -ipdb 3ATV_ADP.pdb -omol2 3ATV_ADP1.mol2 -p 7.4
>
> however as a check I thought I'd try to convert back from mol2 to PDB, but
> when I do I get lots of errors:
>
> babel -imol2 3ATV_ADP1.mol2 -opdb tmp.pdb
The problem arises from that the fact that ADP in 3ATV is residue number 1452,
and the mol2 output is not putting spaces around it. So if you global-replace
'A1452' to 'A 1' in the pdb input, you get a working mol2 file which
round-trips correctly.
This is an openbabel bug: mol2 rows are space-delimited rather than
fixed-length-fields, so
4 O3B -5.4110 17.8230 18.6840 O.co21452 ADP1452 -0.5767
is not a valid line (the atom type reads out as 'O.co21452' which is obviously
not a known one).
Tom
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