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

[Justin Lemkul]

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
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Virginia Tech Department of Biochemistry
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