Fwd: OB writing non-standard atom types?

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Fwd: OB writing non-standard atom types?

Douglas Houston
Just to follow up on this, can someone please try to replicate the  
problem for me using the attached files?


----- Forwarded message from [hidden email] -----
     Date: Fri, 29 Jun 2012 16:50:03 +0100
     From: Douglas Houston <[hidden email]>
  Subject: [Open Babel] OB writing non-standard atom types?
       To: [hidden email]

Hi all,

I've been trying to convert the attached in.pdb file to .mol2 format.  
I happened to be using the -p option:

babel -ipdb in.pdb -omol2 out_p.mol2 -p 7.4

This produces a file that babel chokes on if used as input:

babel -imol2 out_p.mol2 -opdb

==============================
*** Open Babel Warning  in Translate
   Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in ReadMolecule
   This Mol2 file is non-standard. Problem with molecule: in.pdb  
Cannot interpret atom types correctly, instead attempting to interpret  
  atom type: C.cat1490 as elements instead.
==============================
*** Open Babel Warning  in Translate
   Cannot perform atom type translation: table cannot find requested types.

Atom 1 in the mol2 file has been assigned as type C.cat, which  
presumably is causing the problem.

This atom is assigned type C.2 if I use the following command:

babel -ipdb in.pdb -omol2 out_h.mol2 -h

Is it that babel expects a space between the C.cat and the 1490?

If so, that still doesn't explain why I get different atom type  
assignments using -p vs. -h.  I know I can't use -p if I want the  
charges in the output to be sensible (I assign them separately later),  
  but it's now looking like the -p option will also change atom types  
...

Is it simply that the -p option is fully broken and I should just stop  
  using it?

cheers,

Doug


_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



----- End forwarded message -----



_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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in.pdb (2K) Download Attachment
out_p.mol2 (2K) Download Attachment
out_h.mol2 (2K) Download Attachment
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Re: Fwd: OB writing non-standard atom types?

MelissaCoates
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