Hi! Thanks for pointing this out. It is unfortunate that they are missing from the gbsa.itp-file. I will add them, but I do not have time today. If you want to get going, you can add them yourself. The gb-parameters are essentially based on atom hybridization, so for each missing atom you find another that has the same (sp, sp2,sp3) hybridization, and add it to the gbsa.itp-file.
Cheers /Per 21 jan 2011 kl. 13.51 skrev francesca.stanzi...@unina.it: > Hello, > > I try to perform an implicit solvent simulation with Gromacs 4.5.3. version. > I have a system corresponding to 6 peptides generated by Pymol with > simmetrical cell, so I have a single PDB. I used OPLS-AA and i put the N-and > C- termini as NH2 and COOH. My topology file is correct, and is all systems > are included. > > ; Include forcefield parameters > #include "./oplsaa.ff/forcefield.itp" -------> in this .itp file is included > gbsa.itp > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #include "topol_Protein_chain_B.itp" > #include "topol_Protein_chain_C.itp" > #include "topol_Protein_chain_D.itp" > #include "topol_Protein_chain_E.itp" > #include "topol_Protein_chain_F.itp" > > ; Include water topology > #include "./oplsaa.ff/tip3p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include topology for ions > #include "./oplsaa.ff/ions.itp" > > [ system ] > ; Name > Protein > > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > Protein_chain_B 1 > Protein_chain_C 1 > Protein_chain_D 1 > Protein_chain_E 1 > Protein_chain_F 1 > ----------------------------------------------------------------------------- > > When I start my simulations (md_start.mdp) in implicit solvent, i have this > fatal error: > > GB parameter(s) missing or negative for atom type 'opls_912B' > > GB parameter(s) missing or negative for atom type 'opls_267' > > GB parameter(s) missing or negative for atom type 'opls_269' > > GB parameter(s) missing or negative for atom type 'opls_268' > > GB parameter(s) missing or negative for atom type 'opls_270' > > Program grompp, VERSION 4.5.3 > Source code file: grompp.c, line: 1123 > > Fatal error: > Can't do GB electrostatics; the implicit_genborn_params section of the > forcefield is missing parameters for 5 atomtypes or they might be negative. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors. > > ---------------------------------------------------------------------------- > > Controlling these atoms they corresponding to: > > opls_912B= the CA of N-terminal residue > > opls_267= Co in COOH > > opls_268= Oh in COOH > > opls_269= Oc in COOH neutral > > opls_270= H in COOH > > ---------------------------------------- > > in the file gbsa.itp in opls.ff directory these atoms missing. Now, have I > done something wrong? If is all ok, is it possible to create these missing > atoms in the gbsa.itp file? > > thanx, > > francesca stanzione > > -- > 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
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