[gmx-users] No molecules were defined in the system/ No such molecule type Dio

[Justin Lemkul]

On 9/12/12 1:58 AM, sarah k wrote:
> Dear all,
>
> I'm trying to simulate several drug-protein complexes on a clustered
> server. I used PRODRG and editted my .top, .pdb, .gro and posre.itp files.
> Here is the final lines of my .top file:
>
>
>
> ; Include Position restraint file
>
> ; Include Position restraint file
>
> #ifdef POSRES
>
> #include "posre.itp"
>
> #endif
>
>
>
> ; Include water topology
>
> #include "spc.itp"
>
>
>
> ; Include Dio topology
>
> #include "dio.top"
>
>
>
> #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
>
> Nona in water
>
>
>
> [ molecules ]
>
> ; Compound        #mols
>
> Protein_X           1
>
> Dio                 1
>
> SOL             63598
>
>
>
>
>
> The statements are closed with #endif. Yet I recieve "No molecules were
> defined in the system". For the same file I sometimes get "No such molecule
> type Dio" in the first grompp prompt. What's the solution?
>
>

Your topology is misformatted somewhere, either with an #ifdef/#endif block not 
being closed properly or a naming inconsistency somewhere.  The error is not 
apparent from the snippet you've shown, so the best any of us can do is guess at 
this point.

Beware that PRODRG topologies require considerable manual adjustment to be 
considered sufficiently accurate.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
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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