Subject: Re: CCL:Protein PDB to Mol2

From: Richard Gillilan <[email-masked]>
Date: Mon, 03 Feb 2003 18:16:05 -0500

Chris Arthur wrote:

> Hi
>  
> I was wondering if anyone knows how o convert Protein PDB files to 
> MOL2. I've tried using Babel howver it has problems when it comes to 
> recognising the CE, NZ, CZ and SG (and varients of) atom codes instead 
> calling them Du when it gets confused (I assume that...CE - epsilon C 
> , NZ....zeta nitrogen , CZ .....zeta carbon and SG....gamma Sulfur)
>  
> Anyone know of a GPL or GNU program that'll do this happily ?
>  
> Chris 
>  
>  

I recently got OpenBabel to correctly protonate a pdb file for use in 
molecular simulation
(including a GDP group). The code is still really beta for this purpose 
and I had to make
some modifications, but it does seem to work now for polypeptides and is 
actually quite fast.
Check http://sourceforge.net/projects/openbabel/

You are welcome to my modified version of the code. Some mods are 
checked in to the official
version but not all.

Richard Gillilan
MacCHESS, Cornell

---

From: Dimitrios Vlachakis <[email-masked]>
Date: Tue, 4 Feb 2003 12:49:45 +0000

Dear Chris,

Babel does not seem to work fine when it is doing the MOL2 conversion 
of the PDB files. The best way to convert PDB files to MOL2 is to use 
one of the demo molecular modelling software that is available such as 
HyperChem (you can download the demo from www.hyper.com)...

hope that helps

Dimitrios Vlachakis
Cardiff Univeristy