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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_______________________________________________________________________
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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
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