Have a look at http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs
There there's a note: *NB(1):* #include "Ligand.itp" has to be inserted right after ffamber**.itp line and before Protein_*.itp line in *Complex.top*. Are you inserting your gbsa.itp in the *right* place of your top file? Alan On 4 May 2012 14:14, Vedat Durmaz <dur...@zib.de> wrote: > > thanks justin and alan. > > i also had the suspicion that the error is caused by case sensitivity. > simply replacing all atom types from lower to upper case within the > ligand.itp file yields the same error: "missing gb parameters". > > > using the "--disambiguate" option for the parameterization with acpype has > exactly no effect. the generated *_GMX.itp file still contains the same > lower case letters for each atom type. am i doing something wrong? > > > when using the "-atom amber" option (amber99sb instead of gaff), i do get > upper case types, which are not always the same as given with "-a gaff". > however, again, i am told by grompp, that GB parameters are missing for 15 > atom types. and again, most of theese atom types ARE included in the > respective gbsa.itp file (in share/gromacs/top/amber99sb.ff), but few are > not. > > and according to those atom types that are not mentioned in grompp's error > output: about half of them is listed in gbsa.itp while the other ones are > not. > > i can't see any correlation between the atom types listed in my > parameterized molecule's itp-file and the entries in gbsa.itp. > > does anyone have any idea? is there perhaps some other force > field/database file that is checked apart from gbsa.itp?! > > thanks again, > > vedat > > > > Am 04.05.2012 11:23, schrieb Alan: > > 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 >> 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 > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588
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