[gmx-users] Sorting pdb file.

[David van der Spoel]

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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