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

[Paolo Costa]

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 <jalemkul at 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 <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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> >
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
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