PolyBuild

ITP2RTP

Use ITP2RTP to convert ITP files in your current working directory to RTP files. To convert files, just change to the directory containing them, activate the environment you have polyconstruct installed on and run the command. You will be prompted to select which file you would like to convert. The conversion works in a stepwise manner of: ITP->txt->RTP->CSV, and can be stopped at any point.

An example of usage is below:

conda activate polyconstruct-env
ITP2RTP

RTPcharge

Use RTPcharge to post-process the RTP file produced by ITP2RTP. RTPcharge is used to modify partial charges to ensure each monomer contains an integer or 0 net charge. You will be prompted to select which file you would like to process convert, and then the labels on any atoms you want to keep.

An example of usage is below:

conda activate polyconstruct-env
RTPcharge

How monomer charges are adjusted by RTPCharge:

Once the connectivity information has been generated by ITP2RTP, the .rtp file is processed using RTPCharge to modify partial changes to ensure that each monomer contains an integer (or zero) net charge. The user specifies which atoms should be kept, and any unselected atoms are removed. Since removing atoms can alter the net charge, the script calculates the total charge of the remaining atoms and applies proportional adjustments to partial charges to restore the defined charge. Initially, it attempts to distribute the correction within a 5% tolerance of each atom’s original charge. If defined charge cannot be achieved, it increases the tolerance to 10%. If neither threshold is sufficient, the script stops execution, notifying the user. Since these adjustments are done to all the atoms in monomer level, the relative charge distribution across the monomer remains similar. Therefore, the dipole moments, hydrogen bonding patterns, and overall electrostatic potential should not deviate significantly from the original system. However, the charge adjustment tolerance is capped at 10% to limit major alterations to partial charges. If the net charge of a monomer cannot be corrected within this 10% threshold, manual adjustment by the user is required to ensure essential chemical properties are accurately maintained. The final output is a modified .rtp file in the pdb2gmx format required to extract the monomer parameters for the final polymer topology.

Module contents

PolyBuild: A Python library to enable leverage of GROMACS methods for creating polymers from monomers