[gmx-users] Handling of charge field in PDB files by x2top

Steven Kirk Steven.Kirk at htu.se
Wed Nov 16 11:38:39 CET 2005


Can anyone inform me of a way to get atom charge information into a 
topology produced by x2top from a PDB-format input file ? My PDB file 
contains ATOM records with fields laid out as defined in the PDB 
specification, containing the charge in characters 79 and 80 in each 
ATOM record in the form '2+','1-' etc.

Failing this, does anyone know any other (automated) way to get charge 
information into a topology, possibly using another input format ? For 
example, I know that some of the Gromacs programs can GENERATE 
'PDB-like' (e.g. grasp, .pqr) files containing charge information hidden 
in B-factor, etc. fields for use in other programs, but how can I READ 
such files into Gromacs and process the charge information correctly ?

Many thanks in advance,
Steve Kirk
Dr. Steven R. Kirk          <Steven.Kirk at htu.se, S.R.Kirk at physics.org>
Dept. of Computer Science, TMD               http://taconet.webhop.org
Univ. of Trollhattan/Uddevalla   Ph: +46 520 475318 Fax:+46 520 475399
P.O. Box 957 Trollhattan 461 29 SWEDEN

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