Thank you for your answers, I finally added "l" at the end of the names of the atoms, which seemed to be the easiest solution. For most of the computation, having these [bondtypes] like entries was not mandatory, but I wanted to import the topologies in pDynamo, which requires such a "database".
Thank you again ! Baptiste 2013/6/7 Alan <alanwil...@gmail.com> > I may not got the question properly but when I designed ACPYPE, I had > similar issues and for that reason I created this option: > > > -g, --disambiguate disambiguate lower and uppercase atomtypes in GMX top > file > > So try your usual acpype command with "-g" option. > > BTW, acpype -h can show you many more interesting options. > > Alan > > > On 7 June 2013 15:55, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > > 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 > > > > > > -- > Alan Wilter SOUSA da SILVA, DSc > Bioinformatician, UniProt - PANDA, EMBL-EBI > CB10 1SD, Hinxton, Cambridge, UK > +44 1223 49 4588 > -- > 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 > -- 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
