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

[Justin Lemkul]

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)
> --
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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
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