Mol2 to PDB; Nucleotide System. Atom Name lost for some atoms

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Mol2 to PDB; Nucleotide System. Atom Name lost for some atoms

Ben Lowe
Dear OpenBabel community,

I am trying to convert from .mol2 format to .pdb format, whilst
keeping the 'atomname' field (column 3) of the PDB in line with the
mol2 name e.g. C5'.

I have a strand of AAAAAAAAAA bound to a strand TTTTTTTTTT. I'd like
the nucleotides in the PDB to be numbered according to nucleotide
number (1...20).

When I convert the attached PDB file, it works as I hoped for one of
the strands (see second half of the PDB file), but babel seems to not
recognise the first half, and instead default to calling the first
strand simply HETATMs with atomname=element.  e.g. C rather than C5'

I am using
Open Babel 2.2.3 -- Jul 23 2010 -- 07:24:53
babel -imol2 in.mol2 -opdb out.mol2

Any ideas as to what could be going wrong would be very much appreciated,

If file attachments don't work, a dropbox link is here:
https://dl.dropboxusercontent.com/u/3306917/DNA.zip
Thanks,
Ben

------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

2500_1000mM_DNA_justDNA.mol2 (55K) Download Attachment
2500_1000mM_DNA_justDNA.pdb (138K) Download Attachment