On Fri, Apr 17, 2020 at 4:50 PM Paolo Costa <paolo.cost...@gmail.com> wrote:
> 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? * > PDB format only allows 4 characters in a residue name. Rename to something else (in the correct columns of the fixed format) and if that doesn’t fix it, please provide the full screen output from pdb2gmx. -Justin > 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. > -- ========================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ========================================== -- 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.
