Perm-prmtop.py

What it is and why it is important?

We have noticed that potential in AMBER9 is not symmetric with respect to permutations of chemically equivalent atoms e.g. hydrogen atoms in amino group in arginine or oxygen atoms in COO group in glutamate. The source of trouble is in definition of IMPROPER angles. We found a suitable order of atoms for all IMPROPER angles. Correction of appropriate source code in AMBER9 is not a trivial job because the atom order is many times sorted according to some rules to speed up the LEaP program which creates the topology file. Instead of this we can correct the definition of IMPROPER angles in the topology file.

For the new topology file the energy is invariant to permutation of such atoms or groups.

How does it work?

Program perm-prmtop.py written in Python reads topology file created by LEaP finds wrong defined IMPROPER angles, changes the order of appropriate atoms and finally writes the new topology file.

How to use it?

./perm-prmtop.py name-of-topology-file name-of-new-topology-file

Where you can find it?

The program can be downloaded here.

What do you need to remember?

1. The program works for amino acids and nucleic residues present in the following AMBER9 libraries: all_amino02.lib, all_aminont02.lib, all_aminoct02.lib, all_nucleic02.lib and should be modified if some other residues need to be corrected.

2. Names of terminal amino acid residues in topology file created by LEaP are converted to three character format, e.g. NPRO -> PRO therefore you need to rename them before using perm-prmtop.py, e.g. PRO -> NPRO, LYS -> CLYS. In other way these residues will be treated as non terminal ones and e.g. IMPROPER angle defining terminal COO- group still remain wrong.

3. Format of topology file is fixed and for each residue name there are four spaces reserved. If you add C or N to get name of terminal residue, remember to remove a blank space before subsequent name. Here is an example:

line from original topology file created by LEaP:

           PRO ARG GLY SER HIE MET ARG LYS WAT WAT WAT WAT

the same line after modification:

           NPROARG GLY SER HIE MET ARG CLYSWAT WAT WAT WAT