We are making a topology file using the 'perl' command for Charmm2lammps conversion. We created master file by adding parameter file of lipid, carbohydrades, protein & cgenff. In that case, for POPC, it only takes the top & par lipid file and by master file also. If we add water then we cann’t make it. If we add the parameters of water then it is showing-

Info: using wp_edited.pdb instead of wp_edited.crd Info: lx not set: will use extremes Info: ly not set: will use extremes Info: lz not set: will use extremes Info: creating PSF index Info: converting atoms Info: converting bonds Warning: bond parameter 1 for [ ] was not found Info: converting angles Warning: angle parameter 1 for [ ] was not found Info: converting dihedrals Info: converting impropers Info: conversion complete,

It is not working means sometime in the data file which is generated, it is not taking all the atom types of POPC or sometime in case of PAH4 , it is not counting the coordinate of the PHE portion. Actually we are trying to make topology file for a water desalination system using bio-membrane (PAH4)… the water and POPC combined data file…

" 18 atom types 22 bond types 42 angle types 88 dihedral types 1 improper types

-1.402 58.99 xlo xhi -0.033 62.429 ylo yhi -25 70 zlo zhi

Masses

1 0 # 2 1.008 # HL 3 1.008 # HAL1 4 1.008 # HAL2 5 1.008 # HAL3 6 1.008 # HEL1 7 12.011 # CL 8 12.011 # CTL1 9 12.011 # CTL2 10 12.011 # CTL3 11 12.011 # CTL5 ''

the PAH4 data file- " Masses

1 1.008 2 1.008 3 1.008 4 1.008 5 12.011 6 12.011 7 12.011 8 12.011 9 12.011 10 14.007 11 15.999 12 15.999 13 15.999 14 0 15 0 16 0 17 0 18 0 19 0 20 0 21 0 22 0 23 0 24 0 25 0 "

Pair Coeffs

and … ‘’ 253 1 10 -0.47 25.954 34.71 11.514 254 1 1 0.31 24.988 34.736 11.764 255 1 7 0.07 26.154 35.172 10.085 256 1 3 0.09 27.213 35.331 9.953 257 1 8 -0.18 25.526 36.557 9.788 258 1 4 0.09 0 0 0 259 1 4 0.09 0 0 0 260 1 6 0 25.98 37.137 8.356 261 1 6 -0.115 0 0 0 262 1 2 0.115 0 0 0 263 1 6 -0.115 0 0 0 264 1 2 0.115 0 0 0 265 1 6 -0.115 26.892 38.201 5.953 266 1 2 0.115 27.345 38.464 5.008 267 1 6 -0.115 0 0 0 268 1 2 0.115 0 0 0 269 1 6 -0.115 0 0 0 270 1 2 0.115 0 0 0 271 1 5 0.51 25.835 34.062 8.963 272 1 11 -0.51 28.06 35.254 12.228 273 1 10 -0.47 0 0 0 274 1 1 0.31 0 0 0 275 1 7 0.07 0 0 0 276 1 3 0.09 0 0 0 277 1 8 -0.18 0 0 0 278 1 4 0.09 0 0 0 279 1 4 0.09 0 0 0 280 1 6 0 0 0 0 281 1 6 -0.115 0 0 0 282 1 2 0.115 0 0 0 "

In the case of coordinate of MID region ( calixarene part of peptide appended hybrid [4] arene) it always coming zero.