[gmx-users] Case sensitivity in atomtypes

[Baptiste Demoulin]

Hello GMX users,

I have some troubles with overriding parameters. I have generated
parameters for lipids using Lipid11 forcefield for AMBER, based on GAFF,
and Acpype. This forcefield contains atomtypes cA, cB for instance. When I
include the bonded parameters in [bondtypes], [angletypes] sections of my
topology, or alternatively in ffbonded.itp, grompp returns warning
concerning overriding of bonds and angles involving CA, CB, HA, ... (AMBER
atomtypes in capital) by their equivalents in Lipid11 (cA, cB, hA, ...).

WARNING 1 [file ffbonded.itp, line 222]:
  Overriding Bond parameters.

  old: 0.137 435136 0.137 435136     <------- VALUE FOR AMBER FF FOR CB-CB
BOND
  new: cB     cB   1    1.3240e-01    4.9346e+05 <------- VALUE FOR LIPID11
cB-cB


WARNING 2 [file ffbonded.itp, line 225]:
  Overriding Bond parameters.

  old: 0.1404 392459 0.1404 392459
  new: cA     cB   1    1.5080e-01    2.7472e+05


WARNING 3 [file ffbonded.itp, line 227]:
  Overriding Bond parameters.

  old: 0.1381 357314 0.1381 357314
  new: nA     cA   1    1.4990e-01    2.4568e+05


WARNING 4 [file ffbonded.itp, line 228]:
  Overriding Bond parameters.

  old: 0.108 307106 0.108 307106
  new: cA     hA   1    1.0920e-01    2.8225e+05


WARNING 5 [file ffbonded.itp, line 229]:
  Overriding Bond parameters.

  old: 0.14 392459 0.14 392459
  new: cA     cA   1    1.5350e-01    2.5363e+05


WARNING 6 [file ffbonded.itp, line 760]:
  Overriding Angle parameters.

  old: 120 527.184 120 527.184
  new: cA     cA     cA   1    1.1063e+02    5.2894e+02


WARNING 7 [file ffbonded.itp, line 773]:
  Overriding Angle parameters.

  old: 120 527.184 120 527.184
  new: cB     cA     cA   1    1.1144e+02    5.3162e+02


WARNING 8 [file ffbonded.itp, line 783]:
  Overriding Angle parameters.

  old: 117.3 527.184 117.3 527.184
  new: cB     cB     cA   1    1.2342e+02    5.3831e+02


WARNING 9 [file ffbonded.itp, line 788]:
  Overriding Angle parameters.

  old: 120 418.4 120 418.4
  new: cA     cA     hA   1    1.1005e+02    3.8802e+02


WARNING 10 [file ffbonded.itp, line 794]:
  Overriding Angle parameters.

  old: 120 418.4 120 418.4
  new: hA     cA     cB   1    1.1049e+02    3.9355e+02

Aren't Atomtypes supposed to be case sensitive ?

Thank you for your help !

Baptiste