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.
