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

[Justin Lemkul]

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

==================================================