[gmx-users] Generating a PQR file

Mark Abraham mark.abraham at anu.edu.au
Sat Jul 8 03:03:23 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.

Come to think of it, gromacs doesn't use "atomic radii" anywhere except
genion, and if you're planning some Poisson-Boltzmann calculations you
need to be very careful to choose radii that give sensible results with
the type of PB solver you're using. Hacking something up from VDW radii is
a great way to burn CPU cycles for no value.


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