[gmx-users] Sorting pdb file.
vasudevan at iit.edu
Wed Aug 30 00:43:44 CEST 2006
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.
On Aug 29, 2006, at 5:15 PM, David van der Spoel wrote:
> Sheeja vasudevan wrote:
>> 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
>> Thank you for the help!
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
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