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

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 16 11:56:43 CET 2005

On Wed, 2005-11-16 at 11:38 +0100, Steven Kirk wrote:
> Hello,
> 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.
Not without programming, but in x2top it shouldn't be too hard. The pdb
fields are read as B-factor / Occupancy. You want to write a normal
float number (e.g. -2, 1) otherwise reading won't work.

> 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 ?
tpbconv can selectively set charges to zero (for a subset). It wouldn't
be hard to modify it such that it sets charges to something else.

> Many thanks in advance,
> Steve Kirk
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://xray.bmc.uu.se/~spoel

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