[gmx-users] How to include a small organic molecule

[Dallas Warren]

Is that an exact copy of your topology file?  When providing details from commands and files, best if you do copy paste, rather than retyping as you are filtering it through you, which means you can miss things and add errors.

> root folder. But, when I tried to proceed for SD step with grompp then
> one
> error message is showing which is "Fatal Error: Syntax error - File
> Ligand.itp, line 7, Last line read : '[ atomtypes]' Invalid order for
> directive atomtypes.

Explanation of the error is available on the comprehensive list of errors you will encounter with GROMACS at http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

Problem is that you have [defaults] in one of the .itp files, where as it should only be within the forcefield.itp
 
> My input file order in the topology file is
> 
> ;include forcefield paramaeters
> #include "chram27/forecefield.itp"

There is a spelling mistake on the above line, forcefield.itp

> #include "popc.itp"
> #include "ligand.itp"
> 
> .....
> ....
> ....
> 
> [molecules]
> ;compound          #mols
> 
> Protein_chain_A      1
> POPC                     276
> ligand                      1
> SOL                       8748

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.