On Tue, Nov 1, 2011 at 5:44 PM, Justin A. Lemkul <[email protected]> wrote:
> > > Steven Neumann wrote: > > >> >> On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul <[email protected]<mailto: >> [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... >> >> > 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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