[gmx-users] Ligand topology in topol.top

[Steven Neumann]

On Tue, Nov 1, 2011 at 5:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>


You are as always right :) Thanks!

Steven
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