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

Nathan C. Rockwell ncrockwell at ucdavis.edu
Wed Nov 16 18:34:02 CET 2005

I would be concerned that the 'charge' field in PDB format is only 2
characters; that pretty much limits one to formal charges rather than the
partial charges most force fields use.

If the PDB charges are really the ones you want, you'll probably need to do
write something; it might be easiest to generate the topology first and then
have a script to rewrite the charges.


On 11/16/05 2:56 AM, "David van der Spoel" <spoel at xray.bmc.uu.se> wrote:

> 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

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