Dear GROMACS user, I am aware that such error occurs frequently for new users as I am. I am learning how to add new residue in Gromacs; I tried first following a tutorial (https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) and later by creating a benzene, C6H6 molecule, using amber99.ff force field. Everything goes fine without any problems.
For the next step I tried to create residue for a molecule, SnCl6, for which there are no parameters (just for training). Thus, within amber99.ff, I add in the atomtypes.atp the atom Sn with the corresponding mass (the Cl (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ parameters for Sn (again for Cl there are already present). Finally I add in ffbonded.itp the parameters for bond stretch and angle (I calculated them by Gaussian and VFFDT software). I created *my .pdb file* as following: COMPND stannate REMARK 1 File created by GaussView 6.0.16 HETATM 1 Sn SnCl6 0 0.000 0.000 0.000 Sn HETATM 2 Cl1 SnCl6 0 -0.000 0.000 2.502 Cl HETATM 3 Cl2 SnCl6 0 -0.000 2.502 -0.000 Cl HETATM 4 Cl3 SnCl6 0 2.502 0.000 0.000 Cl HETATM 5 Cl4 SnCl6 0 -0.000 -2.502 0.000 Cl HETATM 6 Cl5 SnCl6 0 -2.502 0.000 -0.000 Cl HETATM 7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 Cl END CONECT 1 2 3 4 5 CONECT 1 6 7 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 5 1 CONECT 6 1 CONECT 7 1 and *the .rtp file* which I add in the amber99.ff folder: [ SnCl6 ] [ atoms ] Sn Sn 1.2468 1 Cl1 Cl -0.5411 2 Cl2 Cl -0.5411 3 Cl3 Cl -0.5411 4 Cl4 Cl -0.5411 5 Cl5 Cl -0.5411 6 Cl6 Cl -0.5411 7 [ bonds ] Sn Cl1 Sn Cl2 Sn Cl3 Sn Cl4 Sn Cl5 Sn Cl6 However, although to my eyes I did everything OK, I get such error. *Please, can somebody help me to figure out where I am doing wrong? * Thanks a lot in advance. Paolo Costa -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.