[gmx-users] x2top and bonds. No forcefield type for atom S (2) with 3 bonds

[Justin A. Lemkul]

Vitaly V. Chaban wrote:
> Hi,
> 
> This can be the reason when X2TOP gives the following error:
> "
> Fatal error:
> No forcefield type for atom S (2) with 3 bonds
> "
> ?
> 
> I try to translate PDB of the TFSA anion
>        O    O
>        ||     ||
> F3C-S-N-S-CF3
>        ||     ||
>        O    O
> 
> into topology.
> 
> 
> My PDB contains optimized geometry:
> HEADER    TFSA
> COMPND    TFSA
> AUTHOR    VVC
> ATOM      1  N   TFS     1      -0.000   0.444  -0.008  1.00  0.00
> ATOM      2  S   TFS     1       1.401  -0.440  -0.189  1.00  0.00
> ATOM      3  S   TFS     1      -1.400  -0.438   0.189  1.00  0.00
> ATOM      4  O   TFS     1      -1.236  -1.810  -0.833  1.00  0.00
> ATOM      5  O   TFS     1      -1.284  -1.009   1.805  1.00  0.00
> ATOM      6  O   TFS     1       1.293  -1.026  -1.800  1.00  0.00
> ATOM      7  O   TFS     1       1.233  -1.803   0.845  1.00  0.00
> ATOM      8  C   TFS     1      -2.837   0.628  -0.107  1.00  0.00
> ATOM      9  C   TFS     1       2.836   0.630   0.105  1.00  0.00
> ATOM     10  F   TFS     1      -3.996  -0.097   0.093  1.00  0.00
> ATOM     11  F   TFS     1      -2.805   1.094  -1.408  1.00  0.00
> ATOM     12  F   TFS     1      -2.807   1.698   0.766  1.00  0.00
> ATOM     13  F   TFS     1       2.802   1.099   1.404  1.00  0.00
> ATOM     14  F   TFS     1       2.803   1.698  -0.771  1.00  0.00
> ATOM     15  F   TFS     1       3.996  -0.093  -0.093  1.00  0.00
> END
> 
> and my n2t file is
> 
> C   C   1   C               ; CNT Carbon with one bond
> C   C   2   C   C           : CNT double bonded Carbon
> O   O   1   C               ; CARBONYL OXYGEN (C=O)
> O   OM  1   C               ; CARBOXYL OXYGEN (CO-)
> O   OA  2   C   H           ; HYDROXYL OXYGEN (OH)
> O   OW  2   H   H           ; WATER OXYGEN
> N   N   3   H   C   C       ; PEPTIDE NITROGEN (N OR NH)
> N   NT  3   H   H   C       ; TERMINAL NITROGEN (NH2)
> N   NL  4   C   H   H   H   ; TERMINAL NITROGEN (NH3)
> N   NR5 2   C   C           ; AROMATIC N (5-RING,2 BONDS)
> N   NR5*    3   C   C   H       ; AROMATIC N (5-RING,3 BONDS)
> N   NP  3   C   C   FE      ; PORPHYRIN NITROGEN
> C   C       3   C   O   *       ; BARE CARBON (PEPTIDE,C=O,C-N)
> ; Note that order is importante here because of wildcards.
> C   C3  4   H   H   H   *   ; ALIPHATIC CH3 GROUP
> C   C2  4   H   H   C   *   ; ALIPHATIC CH2 GROUP
> C   C1      4   H   C   *   *   ; ALIPHATIC CH GROUP
> C   CB      3   C   C   C       ; BARE CARBON (5-,6-RING)
> H   H       1   N               ; HYDROGEN BONDED TO NITROGEN
> H   HO      1   O               ; HYDROXYL HYDROGEN
> H   HW      1   OW              ; WATER HYDROGEN
> H   HS      1   S               ; HYDROGEN BONDED TO SULFUR
> H   HC      1   C               ; HYDROGEN BONDED TO CARBON
> S   S       4   C  0.181  N  0.167 O 0.172  O  0.172
> F   F       1   C
> 
> 
> 
> The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
> 3. If I change the string in the N2T to 3 bonds, the topology is
> generated but S-C bond is absent.
> 
> What can be the problem?
> 

I would start with a properly-formatted .n2t file:

http://www.gromacs.org/Documentation/File_Formats/.n2t_File

-Justin

> Thanks.

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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