[gmx-users] Sorting pdb file.

[Sheeja vasudevan]

Hi David,
Thank you replying!!
It is a PDB file containing the coordinates for  atom types SI, OS and  
HO. I want to use it to make an *.itp file for the molecule. I want to  
use it as a single residue.
I have an in house code that would read the information in the pdb  
file, read charge group and other required bonded and non-bonded  
parameters and output a file (hopefully!!)  in itp format. But for this  
I need to have the pdb file in sequence. Currently the file that i got  
from somewhere (??) has atom1 bonded to atoms 370,345,2499 and 1935.  
since i have to define charge groups before running my code it is  
impossible for me to use the pdb file with out sorting it.
I tried x2top but the error was missing force field information.
I was wondering it there is some software that can read my pdb, maybe a  
visualization software, and then allow me to save the atoms in the  
sequence they are bonded. Am i sounding too complicated?
thanks a lot for the help.

Sheeja.

On Aug 29, 2006, at 5:15 PM, David van der Spoel wrote:

> Sheeja vasudevan wrote:
>> Hello
>> I have a pbd file (6240 atoms) which i want to use to  make toplogy  
>> file. However the atoms are not in sequence, that is, atom 1 in the  
>> file is bonded to atoms 2499,345 ,1935 and 370 and so on.. I want to  
>> number them according to their bonding. Is there some program  
>> available to do this?
> you don't say what's in the file!
>
> you could try x2top but it supports only a very small subset of  
> chemistry.
>
>> Thank you for the help!
>> Sheeja.
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>
> --  
> David.
> _______________________________________________________________________ 
> _
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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