The attached 'sed' script can be used quickly and easily convert the DOPC and POPC alpha chain atoms from the all27_lipid (or all32_lipid) convention to the new consistent scheme for all PC lipids used in all36_lipid RTF/PARAM files. The script can be used on most coordinate file formats, esp. PDB and COOR CARD formats (regular and extended). Save the script to a file, and name it cvt_xopc_c27_c36.sed, then convert coord sets via sed -f cvt_xopc_c27_c36.sed old-coords.crd > new coords.crd
Following the coordinate conversion, a new PSF should be constructed, in whatever program is being used (CHARMM, NAMD, ?).
For CHARMM, while the sequences for protein segments are best read from a file, for lipids and water the following is suggested: read sequ popc 80 gener L warn first none last none read sequ tip3 2864 gener W warn noangl nodihe first none last none