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

[Paolo Costa]

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? *

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)