[gmx-users] Ligand topology in topol.top

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
>     Thank you Justin! But actually the last case I provided actually
>     works...
> 

Then the position restraints are not being applied to the ligand.  They can't 
be.  Once the protein [moleculetype] is introduced, all [position_restraints] 
directives immediately after are applied to it.  Try invoking the restraints 
separately, i.e. with "define = -DPOSRES -DPOSRES_LIGAND" and you will get a 
fatal error.

-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

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