[gmx-users] Grompp Fatal Error

[Seonah Kim]

Dear All,

I have a strange error when I use grompp_mpi version.

The error message are the following.


processing coordinates...
Fatal error: number of coordinates in coordinate file (trp_b4md.gro, 3930)
             does not match topology (trp.top, 4677)

When I check the .top file and .gro file, it looks ok.

My trp.top file is


#include "ffgmx.itp"

[ moleculetype ]
; Name            nrexcl
Protein_A           3

[ atoms ]
.
.
.
.

[ system ]
; Name
TC5B in water

[ molecules ]
; Compound        #mols
Protein_A           1
SOL              1493


My trp_b4md.gro starts


TC5B in water
 3930
    1ASN      N    1   1.151   2.385   1.347  0.2000 -0.1934  0.2965
    1ASN     H1    2   1.217   2.451   1.313  0.1038 -0.1224  0.2472
    1ASN     H2    3   1.057   2.419   1.349  0.3302  0.1410  1.3608
    1ASN     H3    4   1.177   2.372   1.443 -0.2137  0.3114  0.4801
    1ASN     CA    5   1.165   2.262   1.268 -0.2618 -0.2449  0.2931
    1ASN     CB    6   1.134   2.294   1.122 -0.7929 -0.6031  0.3205
    1ASN     CG    7   1.097   2.171   1.039  0.2168 -0.4420 -0.3929
    1ASN    OD1    8   1.150   2.140   0.932  0.3514  0.1799 -0.5127
    1ASN    ND2    9   0.991   2.104   1.084  0.3169 -0.2285  0.1738
    1ASN   HD21   10   0.924   2.133   1.152  1.0688  1.4726  0.2515
    1ASN   HD22   11   0.995   2.007   1.060  0.6780 -0.4384  1.0670
    1ASN      C   12   1.302   2.198   1.292 -0.0064  0.2139  0.0576
    1ASN      O   13   1.313   2.137   1.398  0.4270 -0.1584 -0.1947
    2LEU      N   14   1.411   2.236   1.226 -0.0100 -0.0694 -0.1158
    2LEU      H   15   1.423   2.330   1.193 -1.1687 -0.7479 -2.7571
    2LEU     CA   16   1.535   2.157   1.227  0.3282  0.4507 -0.1158
    2LEU     CB   17   1.633   2.230   1.136  0.3483  0.0231 -0.4388
    2LEU     CG   18   1.651   2.377   1.174  0.5486 -0.1992  0.3373
    2LEU    CD1   19   1.774   2.403   1.262  0.0986  0.3852  0.8005
    2LEU    CD2   20   1.658   2.455   1.043 -0.0847 -0.2561  0.2669
    2LEU      C   21   1.598   2.106   1.357  0.2044  0.1330 -0.1782
    2LEU      O   22   1.668   2.005   1.349 -0.4793 -0.3072 -0.7101

Would you tell me what is my problem?

Thanks.

Seonah Kim.