[gmx-users] Fatal error:No molecules were defined in the system

[Nilesh Dhumal]

Hello,

For grompp

grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr

I get the error" Fatal error:No molecules were defined in the system"

Here I pasted initial part of test.top file.




; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
 1               3               yes             0.5     0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_991   Cu    29	63.54600    1.098       A    3.114e-01    0.02092e+00
 opls_993   OA    8     15.99940    -0.665       A    3.033e-01   
0.401664e+00
 opls_994   OB    8     15.99940    -0.665       A    3.033e-01   
0.401664e+00
 opls_995   CA    6     12.0110      0.778       A    3.473e-01   
0.39748e+00
 opls_996   CB    6     12.0110     -0.092       A    3.473e-01   
0.39748e+00
 opls_997   CC    6     12.0110     -0.014       A    3.473e-01   
0.39748e+00
 opls_998   HM    1      1.0080      0.109       A    2.846e-01   
0.06276e+00

[ moleculetype ]
; Name            nrexcl
 BTC             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
  1    opls_993      1    BTC    OA       1    -0.665    15.99940
  2    opls_995      1    BTC    CA       2     0.778    12.01100
  3    opls_996      1    BTC    CB       3    -0.092    12.01100
  4    opls_997      1    BTC    CC       4    -0.014    12.01100
  5    opls_998      1    BTC    HM       5     0.109     1.00800
  6    opls_997      1    BTC    CC       6    -0.014    12.01100
  7    opls_998      1    BTC    HM       7     0.109     1.00800
  8    opls_993      1    BTC    OA       8    -0.665    15.99940
  9    opls_995      1    BTC    CA       9     0.778    12.01100
 10    opls_996      1    BTC    CB      10    -0.092    12.01100
 11    opls_997      1    BTC    CC      11    -0.014    12.01100
 12    opls_998      1    BTC    HM      12     0.109     1.00800
 13    opls_993      1    BTC    OA      13    -0.665    15.99940
 14    opls_995      1    BTC    CA      14     0.778    12.01100
 15    opls_996      1    BTC    CB      15    -0.092    12.01100
 16    opls_994      1    BTC    OB      16    -0.665    15.99940
 17    opls_994      1    BTC    OB      17    -0.665    15.99940
 18    opls_994      1    BTC    OB      18    -0.665    15.99940
 19    opls_993      1    BTC    OA      19    -0.665    15.99940
 20    opls_995      1    BTC    CA      20     0.778    12.01100

Is there any error in .top file?



Thanks,

Nilesh