[gmx-users] Ligand topology in topol.top

[Steven Neumann]

On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul <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...


Steven
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