[gmx-users] Generating a PQR file

Mark Abraham mark.abraham at anu.edu.au
Sat Jul 8 02:59:43 CEST 2006

> Hello everyone,
> I would like to create a PQR file (basically a PDB file but with charges
> in
> B-field and radii in occupancy field). However, there doesn't seem to be
> any
> straightforward way to do this.

Probably not, unless someone else has had the problem before :-)

> I noticed that this could be done with editconf, however this is difficult
> given
> the way I have my topologies set up. I have a separate topology (.itp) for
> each
> molecule in my system (dna, water, counterions, etc.). Thus, the atom
> numbers
> in these files are not unique. Thus, there is no good way of feeding in
> the
> charges to editconf by listing the charge for each atom number. Is there a
> way
> to extract this information from a .tpr file?

gmxdump -s file.tpr gets you a dump, but you'd need to write a script to
get the relevant parts of that out and merge it with a .pdb file.


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