[gmx-users] Strange Fatal error

[K.A.Feenstra]

Andrew Horsfield wrote:
> 
> 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?

You have defined a moleculetype with 15 atoms, but you have not defined
a system (with the [ system ] directive). See manual for obligatory
entries in your .top file. It is something like:
--example--
[ system ]
; Name
Small molecule

[ molecules ]
; Compound        #mols
DRG		1
--example--

NOTE: the system name ('small molecule') is irrelevant, but it is
still obligatory, i.e. if you specify no name, it won't work.


[PS: Andrew, sorry you get this twice, I forgot to send it to the list]

Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
| / \ / \'| | | Tel +31 50 363 4327                    Nijenborgh 4 |
|(   |   )| | | Fax +31 50 363 4800               9747 AG Groningen |
| \_/ \_/ | | | http://md.chem.rug.nl/~anton        The Netherlands |
|             | "It Costs Too Much If It Costs a Lot" (Magnapop)    |
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