Hi there, look at 'acpype -h', in particular:
-g, --disambiguate disambiguate lower and uppercase atomtypes in GMX top file Alan On 3 May 2012 14:34, Vedat Durmaz <dur...@zib.de> wrote: > > hi guys, > > i'm trying to simulate some receptor ligand system with implicit solvent > using gbsa in order to get a quick folding of some tens of N-terminal > peptides. this works pretty well with the target only applying the > amber99sb FF. as soon as i try to simulate it together with the ligand > which was parameterized with acpype (using amber-antechamber), i get the > following error at the grompp step: > > GB parameter(s) missing or negative for atom type 'cc' > GB parameter(s) missing or negative for atom type 'n' > ... > Fatal error: > Can't do GB electrostatics; the implicit_genborn_params section of the > forcefield is missing parameters for 15 atomtypes or they might be negative. > > > the atom types in the error output are exactly those listed in the [ atom > types ] section of the ligand's topology file created with > acpype/antechamber. however, the atom types mentioned here ARE listed in > the respective gbsa.itp file which looks like this: > > > [ implicit_genborn_params ] > > ; atype sar st pi gbr hct > ... > CC 0.172 1 1.554 0.1875 0.72 ; C > > > does anybody know how to handle this problem? > > and is there someone that can tell me how (with which parameter values) to > add GAFF atom types like e.g. "ss", "hn", "hx", "os" to the gbsa.itp file? > > thanks in advance and take care > > vedat durmaz > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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