On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin <bat.demou...@gmail.com>wrote:
> 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 ? > Probably not, when pdb2gmx was designed. Using a case-sensitive tool like sed (or perl, or python) to re-name "cA" to "LcA" or something is probably the best solution. But don't break the fixed-column requirements of your coordinate files! Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
