BMP (LBPA) topologies, parameters, configurations, and related scripts
Contents:
000README
PDB files for LBPA configurations:
2-2R-RLBPA.pdb
2-2R-SLBPA.pdb
2-2S-SLBPA.pdb
3-3R-RLBPA.pdb
3-3R-SLBPA.pdb
3-3S-SLBPA.pdb
Python script to check and convert R/S handedness:
check_chirals.py
Slipids topologies:
Slipids_2-2LBPA.itp
Slipids_3-3LBPA.itp
Charmm36 topologies:
top_all36_2-2LBPA.rtf
top_all36_3-3LBPA.rtf
Notes:
1) All bonded terms are already included in Slipids and the charges are calculated based on the protocol used in Slipid parametrization
See the comments in the itp files.
2) One has to change the molecule name if one wants to simulate a mixture of 3-3 and 2-2 isomers.