This Python script allows you to convert an Amber (version 7 and higher), topology file (.prmtop) into a pqr format. This script takes as input the pdb of the system, the prmtop file, the output pqr file name and, optionally, a VMD-like atom selection string. To parse the pdb and apply the selection the ProDy package is used and must be previously installed: ProDy is an excellent tool to manipulate MD trajectories and pdb files and can be dowloaded from www.csb.pitt.edu/prody .
The script typical application is in converting a system used in a MD simulation to perform computations with DelPhi or protonate a system by tleap (AmberTools) and then using DelPhi on it.The presence of the atom selection string allows the user to remove in one step all the undesired components of the system (e.g. waters).
A typical usage example is:
python getPQRfromPrmtop.py sys.pdb box.prmtop sys_prot.pqr "protein"
where "protein" is the VMD-like atom selection string to remove all but the protein atoms. Another useful example to retain protein atoms, DNA atoms and those belonging to the ligand LIG is:
python getPQRfromPrmtop.py sys.pdb box.prmtop sys_dna_lig.pqr "protein or nucleic or resname LIG"