Hi Justin, I could fix the issue.
Thanks again for your help. Paolo Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul <jalem...@vt.edu> ha scritto: > > > On 4/17/20 5:25 PM, Paolo Costa wrote: > > Hi Justin, > > > > thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my > > stannate.pdb and also to stannate.rtp. But still I get the error. > > Here the output file of from pdb2gmx: > > > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b > > Reading stannate.pdb... > > WARNING: all CONECT records are ignored > > Read 'stannate', 7 atoms > > Analyzing pdb file > > Splitting chemical chains based on TER records or chain id changing. > > There are 1 chains and 0 blocks of water and 1 residues with 7 atoms > > > > chain #res #atoms > > 1 ' ' 1 7 > > > > All occupancy fields zero. This is probably not an X-Ray structure > > Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp > > Atomtype 68 > > Reading residue database... (amber99) > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp > > Residue 93 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp > > Residue 94 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp > > Residue 110 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp > > Residue 126 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp > > Residue 127 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb > > Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb > > Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb > > > > Back Off! I just backed up topol.top to ./#topol.top.19# > > Processing chain 1 (7 atoms, 1 residues) > > > > Warning: Starting residue SnC0 in chain not identified as > Protein/RNA/DNA. > > This chain lacks identifiers, which makes it impossible to do strict > > classification of the start/end residues. Here we need to guess this > residue > > should not be part of the chain and instead introduce a break, but that > will > > be catastrophic if they should in fact be linked. Please check your > > structure, > > and add SnC to residuetypes.dat if this was not correct. > > > > Problem with chain definition, or missing terminal residues. > > This chain does not appear to contain a recognized chain molecule. > > If this is incorrect, you can edit residuetypes.dat to modify the > behavior. > > 8 out of 8 lines of specbond.dat converted successfully > > > > ------------------------------------------------------- > > Program: gmx pdb2gmx, version 2018.1 > > Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) > > > > Fatal error: > > Residue 'SnC' not found in residue topology database > > > > *Thanks a lot for helping!* > > Without seeing the contents of the PDB file and stannate.rtp, there's > not much to go on here. > > -Justin > > -- > ================================================== > > 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. > -- 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.