[gmx-users] Position Restraints of one of the moleculetpye

[Steven Neumann]

On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/29/12 6:52 AM, Steven Neumann wrote:
>
>> Ok. My topology:
>>
>> ; Include forcefield parameters
>> #include "./charmm27.ff/forcefield.itp"
>>
>> ; Include ligand topology
>> #include "ligand1.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_1
>> #include "posre_ligand1.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand2.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_2
>> #include "posre_ligand2.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand3.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_3
>> #include "posre_ligand3.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand4.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_4
>> #include "posre_ligand4.itp"
>> #endif
>>
>>
>> ; Include ligand topology
>> #include "ligand5.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_5
>> #include "posre_ligand5.itp"
>> #endif
>>
>> ; Include ligand topology
>> #include "ligand6.itp"
>>
>> ; Include Position restraint file
>> #ifdef POSRES_6
>> #include "posre_ligand6.itp"
>> #endif
>>
>> ; Include water topology
>> #include "./charmm27mod.ff/tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>    1    1       1000       1000       1000
>> #endif
>>
>> ; Include topology for ions
>> #include "./charmm27.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound        #mols
>> ligand1               1
>> ligand2               1
>> ligand3               1
>> ligand4               1
>> ligand5               1
>> ligand6               1
>> SOL              4617
>>
>>
>> Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other
>> information
>> is the same
>>
>> posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.
>>
>> Then when I grompp:
>>
>> Syntax error - File ligand2.itp, line 7
>> Last line read:
>> '[ atomtypes ] '
>> Invalid order for directive atomtypes
>>
>> Any suggestions appreciated,
>>
>>
> Once you declare a [moleculetype], the other force field-level directives
> cannot be called.  If all the ligand topologies are the same, remove
> [atomtypes] from all but the first.
>
>
> -Justin
>

Thanks Justin. Removing [pairtypes] and [atomtypes] from all but not the
first helped.

Steven



> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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