On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul <[email protected]> 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> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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