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

[Justin A. Lemkul]

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

-- 
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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

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