[gmx-users] Ligand topology in topol.top

[Justin A. Lemkul]

Steven Neumann wrote:
> Hi Guys,
>  
> I am using Charmm27 ff for my protein and ligand system. I used 
> SwissParam to generate the topology for my ligand. I included the 
> obtained topology of my ligand as in Justin tutorial:
>  
> 
> ; Include Position restraint file
> 
> #ifdef POSRES
> 
> #include "posre.itp"
> 
> #endif
> 
> ; Include ligand topology
> 
> #include "ligand.itp"
> 
> ; Ligand position restraints
> 
> #ifdef POSRES
> 
> #include "posre_ligand.itp"
> 
> #endif
> 
> ; Include water topology
> 
> #include "charmm27.ff/tip3p.itp"
> 
>  
> When I wanted to run NVT I obtained:
>  
> Fatal error:
> Syntax error - File egcg.itp, line 7
> Last line read:
> '[ atomtypes ] '
> Invalid order for directive atomtypes
>  
>  
> However when I included my topology as:
>  
> 
> ; Include forcefield parameters
> 
> #include "charmm27.ff/forcefield.itp"
> 
> #include "ligand.itp"
> 
> [ moleculetype ]
> 
> ; Name nrexc
> 
> ......................
> 
> ; Include Position restraint file
> 
> #ifdef POSRES
> 
> #include "posre.itp"
> 
> #endif
> 
> ; Ligand position restraints
> 
> #ifdef POSRES
> 
> #include "posre_egcg.itp"
> 
> #endif
> 
> ; Include water topology
> 
> #include "charmm27.ff/tip3p.itp"
> 
> ,,,,
>  
> Everything seems to be ok!
> Any clue why is that?
>  

The topology must follow a defined order.  Please consult Chapter 5 of the 
manual for the required hierarchy.  Of course, the latter case will also not 
work, because you've introduced ligand position restraints after the protein 
[moleculetype], so if invoked, they will cause a different fatal error.

The Gromacs site also has more on these types of errors, as well as the list 
archive, where this error has been posted and solved hundreds of times.

-Justin

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

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

========================================