[gmx-users] grompp gives "no molecules were defined in the system"

[Justin A. Lemkul]

Marysa van den Berg wrote:
> Hi,
>  
> The number of atoms in the second line of my .gro file are correct, I 
> checked that.
>  
> This is what my topology file says in the beginning:
>  
> [ moleculetype ]
> ; Name      nrexcl
> Protein      3
>  
> No changes here after the solvation.
>  
> At the end after the [ atoms ] directive:
>  
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>  
> ; Strong po
> sition restraints for InflateGro
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> endif
>  

Here's the problem.  To end the #ifdef statement, you need "#endif", not 
"endif."  Since you haven't closed the #ifdef, nothing is being found after this 
point in the topology (assuming you're not specifying "define = -DSTRONG_POSRES" 
in the .mdp file, which you only want at certain times).

-Justin

> ; Include DPPC chain topology
> #include "dppc.itp"
>  
> ; Include water topology
> #include "spc.itp"
>  
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx    fcy  fcz
>   1    1   1000 1000 1000
> #endif
>  
> ; Include generic topology for ions
> #include "ions.itp"
>  
> [ system ]
> ; Name
> Protein
>  
> [ molecules ]
> ; Compound #mols
> Protein        1
> DPPC          242
> SOL           48333
>  
> The only thing in the topology that changed after the solvation, was 
> adding the watermolecules in the [ molecules ] section (SOL 48333)
> What could be the problem?
>  
> Thanks,
>  
> Marysa
> 
> ------------------------------------------------------------------------
> Ontdek nu Windows phone. De smartphone van dit moment 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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