On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul <[email protected]> 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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