Ok! The problem doesn't really come from gromacs so. It's my side-chain positioning software which made this... I'll try to fix it.
Thank you very much. Pierre THEVEVENET ----- Mail original ----- De: "Justin A. Lemkul" <[email protected]> À: "Discussion list for GROMACS users" <[email protected]> Envoyé: Mardi 17 Janvier 2012 15:30:08 Objet: Re: [gmx-users] grompp g96angle types error [email protected] wrote: > The problem seems to be between 3 S of CYS residues. I only use the 20 usual > residues and with no modifications. > An angle involving three S atoms? That should never occur. > Where is the ffbonded.itp file? It's in $GMXLIB, i.e. the /share/gromacs/top subdirectory of your Gromacs installation. If the problematic angle is indeed S-S-S, I guarantee you won't find it there, though. -Justin > > Thank you, > > > Pierre THEVENET > > ----- Mail original ----- > De: "Justin A. Lemkul" <[email protected]> > À: "Discussion list for GROMACS users" <[email protected]> > Envoyé: Mardi 17 Janvier 2012 15:12:58 > Objet: Re: [gmx-users] grompp g96angle types error > > > > [email protected] wrote: >> Dear all, >> >> I launch those commands for few models : >> >> pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p >> 2it7-10_bestene1mc-SC.top -ignh -missing >> >> editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d >> 2.0 -c -bt cubic >> >> grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o >> 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp >> >> and at the grompp command I obtain : >> >> checking input for internal consistency... >> calling /lib/cpp... >> processing topology... >> Generated 165 of the 1596 non-bonded parameter combinations >> ERROR 0 [file "2it7-10_bestene1mc-SC.top", line 1242]: >> No default G96Angle types >> Excluding 3 bonded neighbours for Protein 1 >> NOTE: >> System has non-zero total charge: 1.000000e+00 >> >> processing coordinates... >> double-checking input for internal consistency... >> renumbering atomtypes... >> converting bonded parameters... >> # G96BONDS: 254 >> # G96ANGLES: 367 >> # PDIHS: 149 >> # IDIHS: 108 >> # LJ14: 436 >> >> I don't understand the meaning of: No default G96Angle types. >> >> All my files are generated by the same way, with the same softwares, and the >> sames options. All the models are done by the same software so the .pdb file >> only the coordinates of the protein change for one model to another. >> >> Can you help me? >> > > The error message indicates that angle parameters do not exist in the chosen > force field for a certain sequence of atoms. This would be highly unusual > for a > standard protein. Are you using any custom residues? The error message > indicates the line in the .top that is causing the problem. Look it up, find > which atoms it corresponds to, and check ffbonded.itp to verify that suitable > parameters are indeed not present. If you're using some kind of custom > residue > or nonstandard composition of atoms, then you'll likely have to parameterize > the > missing term(s) yourself. > > -Justin > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
