[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

[ahmet yıldırım]

Dear users,

pdb2gmx -f xxx.pdb
water:spc
forcefield:43a1
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
*Fatal error:*
number of coordinates in coordinate file (solvated.gro, 106523) does not
match topology (topol.top, 106553)
I look at gmx-user search. But I dont be able to solved the problem. Then I
look at conf.gro and box.gro. I recognised the there is not the TRS ligand
in the box.gro file. What reason?

Thanks in advance

*conf.gro:*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5354
    2GLN      N    1   1.458  -1.158   0.739
    2GLN     H1    2   1.520  -1.083   0.763
...
  485HOH    HW1 5333   0.221  -3.864  -2.291
  485HOH    HW2 5334   0.303  -3.946  -2.407
    1EDO  OAB      1   0.625  -3.071  -0.171
    1EDO  HAA      2   0.698  -3.048  -0.107
    1EDO  CAA      3   0.596  -3.211  -0.163
    1EDO  CAC      4   0.486  -3.247  -0.261
    1EDO  OAD      5   0.365  -3.179  -0.224
    1EDO  HAB      6   0.292  -3.203  -0.288
    1TRS  O1       1   1.825  -3.900   0.047
    1TRS  HAA      2   1.853  -3.860  -0.040
    1TRS  C1       3   1.712  -3.977   0.028
    1TRS  C        4   1.659  -4.044   0.150
    1TRS  C3       5   1.576  -3.946   0.226
    1TRS  O3       6   1.634  -3.824   0.256
    1TRS  HAC      7   1.569  -3.768   0.307
    1TRS  N        8   1.582  -4.159   0.113
    1TRS  HAE      9   1.547  -4.204   0.195
    1TRS  HAF     10   1.505  -4.131   0.056
    1TRS  HAD     11   1.639  -4.223   0.062
    1TRS  C2      12   1.776  -4.085   0.233
    1TRS  O2      13   1.887  -4.122   0.160
    1TRS  HAB     14   1.961  -4.148   0.222
   8.13100   7.04165  13.54850   0.00000   0.00000  -4.06550   0.00000
0.00000   0.00000





-- 
Ahmet YILDIRIM
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