If you use these parameters for any research, please cite the following paper:


	GAFFlipid: a General Amber Force Field for the accurate molecular
	dynamics simulation of phospholipid

	C. J. Dickson, L. Rosso, R. M. Betz, R. C. Walker and I. R. Gould

	Soft Matter, 2012, 8, 9617-9627

	DOI: 10.1039/c2sm26007g

It is intended to incorporate these parameters with lipid11, creating
a new, updated modular AMBER lipid force field in the near future.

##################  GAFFlipid parameters #################################

LIB files are provided folder:

./parameters

POPE -> PPE.lib

Please load the parameters into leap as follows:

	>source leaprc.gaff
	>source GAFFlipid.dat
	>loadamberparams GAFFlipid.frcmod
	>loadoff PPE.lib

########################  PDB files  #####################################

PDB files from the end of the production runs for each system size
(72, 288 and 2x288 lipids) are provied in the folder:

./pdb

These may be directly loaded into leap provided the relevant parameters
are first loaded as outlined above.

#############  Usage with charmm lipid pdb files  ########################

PDB files created with the CHARMM membrane builder 
(http://www.charmm-gui.org/?doc=input/membrane) 
may be loaded into leap using the LIB files in the folder:

./charmm_compatible

Note that these LIB files are different to those in the parameters folder.

Prior to loading into leap, residue names of waters, ions, POPC and POPE
must be changed to amber compatible naming.

 - Please run the script convert_charmm.x as follows:
	     ./convert_charmm.x input_pdb output_pdb

   where input_pdb is the membrane created from the charmm membrane
   builder and output_pdb is the name of the output file to create.

 - Note, you may have to add executable permission to this script:
	     chmod +x convert_charmm.x

[ AMBER only reads the first three letters of a residue name, hence
  POPC and POPE will be indistinguishable. Thus POPC is renamed PPC;
  likewise POPE is renamed PPE. ]

