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

Paolo Costa paolo.costa85 at gmail.com
Fri Apr 17 23:25:52 CEST 2020


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!*

Paolo

Il giorno ven 17 apr 2020 alle ore 22:55 Justin Lemkul <jalemkul at vt.edu> ha
scritto:

> On Fri, Apr 17, 2020 at 4:50 PM Paolo Costa <paolo.costa85 at gmail.com>
> wrote:
>
> > Dear GROMACS user,
> >
> > I am aware that such error occurs frequently for new users as I am.
> > I am learning how to add new residue in Gromacs; I tried first following
> a
> > tutorial (
> > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ )
> > and later by creating a benzene, C6H6 molecule, using amber99.ff force
> > field. Everything goes fine without any problems.
> >
> > For the next step I tried to create residue for a molecule, SnCl6, for
> > which there are no parameters (just for training). Thus, within
> amber99.ff,
> > I add in the atomtypes.atp the atom Sn with the corresponding mass (the
> Cl
> > (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ
> > parameters for Sn (again for Cl there are already present). Finally I add
> > in ffbonded.itp the parameters for bond stretch and angle (I calculated
> > them by Gaussian and VFFDT software).
> >
> > I created *my .pdb file* as following:
> > COMPND    stannate
> > REMARK    1  File created by GaussView 6.0.16
> > HETATM    1  Sn   SnCl6  0       0.000   0.000   0.000
> >  Sn
> > HETATM    2  Cl1  SnCl6  0      -0.000   0.000   2.502
> >  Cl
> > HETATM    3  Cl2  SnCl6  0      -0.000   2.502  -0.000
> >  Cl
> > HETATM    4  Cl3  SnCl6  0       2.502   0.000   0.000
> >  Cl
> > HETATM    5  Cl4  SnCl6  0      -0.000  -2.502   0.000
> >  Cl
> > HETATM    6  Cl5  SnCl6  0      -2.502   0.000  -0.000
> >  Cl
> > HETATM    7  Cl6  SnCl6  0      -0.000  -0.000  -2.502
> >  Cl
> > END
> > CONECT    1    2    3    4    5
> > CONECT    1    6    7
> > CONECT    2    1
> > CONECT    3    1
> > CONECT    4    1
> > CONECT    5    1
> > CONECT    6    1
> > CONECT    7    1
> >
> >
> > and *the .rtp file* which I add in the amber99.ff folder:
> > [ SnCl6 ]
> > [ atoms ]
> > Sn    Sn    1.2468  1
> > Cl1   Cl   -0.5411  2
> > Cl2   Cl   -0.5411  3
> > Cl3   Cl   -0.5411  4
> > Cl4   Cl   -0.5411  5
> > Cl5   Cl   -0.5411  6
> > Cl6   Cl   -0.5411  7
> > [ bonds ]
> > Sn Cl1
> > Sn Cl2
> > Sn Cl3
> > Sn Cl4
> > Sn Cl5
> > Sn Cl6
> >
> > However, although to my eyes I did everything OK, I get such error.
> > *Please, can somebody help me to figure out where I am doing wrong? *
> >
>
> PDB format only allows 4 characters in a residue name. Rename to something
> else (in the correct columns of the  fixed format) and if that doesn’t fix
> it, please provide the full screen output from pdb2gmx.
>
> -Justin
>
>
> > Thanks a lot in advance.
> >
> > Paolo Costa
> >
> > --
> > 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)
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-request at 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
>
> 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)


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