[gmx-users] Topolbuild

[Alex]

Dear all,

Using topolbuild the *.gro and *.top file for a GPS molecule (C_6H_14O_5Si)
were generated. In the GPS molecule there is a --Si(OH)3 group in which the
Si and H are indeed the atoms which produce problem in the topol file.
The Si and that H are named like below in the [ atom ] section ;

 [ atoms ]
;  nr    type   resnr   residu   atom   cgnr    charge      mass
    1    opls_154     1       GPS       O    1   0.00000  15.99940
;   0.0000000
    2         H??     1       GPS       H    1   0.00000   1.00800
;   0.0000000
    3          SI     1       GPS      Si    1   0.00000  28.08000
;   0.0000000
    4    opls_136     1       GPS       C    2   0.00000  12.01100
;   0.0000000
    5    opls_140     1       GPS       H    2   0.00000   1.00800
;   0.0000000

And then the bond and angle sections wherever those two atoms are involved
are empty like below;
 [ bonds ]
;   ai  aj   funct      b0          kb
      24    23   1     0.10880      284512.       ;     H-     C
      4     6   1     0.10900      284512.       ;     C-     H
       4     3                                    ;     C-    Si
      14    13                                    ;     H-     O
      13     3                                    ;     O-    Si
       3     1                                    ;    Si-     O
       3    15                                    ;    Si-     O

Any suggestion to overcome the problem would be highly appreciated.

Best regards,
Alex