[gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6

[Paolo Costa]

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 <jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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-- 
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)