[gmx-users] Strange Fatal error

[Andrew Horsfield]

Hi,

I am trying to do something very simple! I have a small molecule that I 
have relaxed using DMol3. Using the final coordinates, I produced a PDB 
file. I fed this to PRODRG, and got back a gro and a top file. I used 

 editconf -f pterin.gro -o relax.gro -d 1.0

to add a box, and then used

 grompp -f relax-tmpl.mdp -po relax.mdp -c relax.gro -p relax.top -o relax.tpr

to produce the input file. But I got the error:

Fatal error: number of coordinates in coordinate file (relax.gro, 15)
             does not match topology (relax.top, 0)

I have checked the files, and can see no problem. For the record, the gro 
file contains:

 PRODRG COORDS
   15
    1DRG     HA    1   1.153   1.212   1.067
    1DRG      N    2   1.231   1.175   1.118
    1DRG      C    3   1.361   1.197   1.064
    1DRG      O    4   1.375   1.259   0.960
    1DRG      C    5   1.466   1.137   1.150
    1DRG      N    6   1.593   1.149   1.110
    1DRG      C    7   1.685   1.096   1.190
    1DRG      C    8   1.650   1.032   1.310
    1DRG      N    9   1.524   1.019   1.351
    1DRG      C   10   1.429   1.071   1.270
    1DRG      N   11   1.299   1.056   1.311
    1DRG      C   12   1.206   1.108   1.235
    1DRG      N   13   1.075   1.100   1.274
    1DRG     HC   14   1.050   1.051   1.358
    1DRG     HB   15   1.004   1.145   1.220
   2.68100   2.24000   2.39800

and the top file starts:

#include "ffgmx.itp"
 
 [ moleculetype ]
 ;name nrexcl
DRG      3
;
 [ atoms ]
 ;  nr  type resnr resid  atom  cgnr charge
     1     H     1 DRG      HA     1    0.000
     2  NR6*     1 DRG       N     2    0.000
     3    CB     1 DRG       C     3    0.380
     4     O     1 DRG       O     3   -0.380
     5    CB     1 DRG       C     4    0.000
     6   NR6     1 DRG       N     5    0.000
     7  CR61     1 DRG       C     6    0.000
     8  CR61     1 DRG       C     7    0.000
     9   NR6     1 DRG       N     8    0.000
    10    CB     1 DRG       C     9    0.000
    11   NR6     1 DRG       N    10    0.000
    12    CB     1 DRG       C    11    0.000
    13    NT     1 DRG       N    12   -0.830
    14     H     1 DRG      HC    12    0.415
    15     H     1 DRG      HB    12    0.415

There are clearly 15 atoms in both files. So what does the error message 
mean?

Cheers,

Andrew