It was a typos. In the .pdb file I wrote SnC as residue name, while in .rtp file it was still written SnCl. That's why the error. Thanks a lot again.
Paolo Il dom 19 apr 2020, 22:05 Justin Lemkul <jalem...@vt.edu> ha scritto: > > > On 4/19/20 3:47 PM, Paolo Costa wrote: > > Hi Justin, > > > > I could fix the issue. > > > > Thanks again for your help. > > And in the spirit of helping others that use this mailing list, what > exactly was the problem and how did you solve it? > > -Justin > > > 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. > >> > > > > -- > ================================================== > > 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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