Perm-prmtop.py

What it is and why it is important?

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

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

How does it work?

Program perm-prmtop.py, written in Python reads topology file created by LEaP, finds wrongly 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 and nucleic acid 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. The names of terminal amino acid residues in the initial 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. Otherwise these residues will be treated as non terminal ones and e.g. the IMPROPER angle defining terminal the geometry of the COO- group will still be wrong.

3. The 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