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, Steven On Mon, May 28, 2012 at 5:25 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 5/28/12 10:48 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> I am fighting with the position restraints. My system cosnsists of 6 >> ligands - >> all of them have the same topology - ligand.itp. I want to: >> >> 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, >> posre >> ligand1.itp >> 2. Restrain 5 of them and pull one of them away. >> >> Here I came across some difficulties. >> >> I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp >> >> and by index files I create an index of the ligands I wan to restrain. >> Each my >> ligands has 46 atoms. When I process to grompp: >> >> Atom index (256) in position_restraints out of bounds (1-46). >> This probably means that you have inserted topology section >> "position_restraints >> >> Shall I rename Ligands as different residue names? If my posre includes >> 1-46 >> atom all ligands are restraints? How to restrain just 5 out of 6 of them? >> >> > Position restraints are applied on a per-moleculetype basis. If you have > six copies of a ligand, the only way to do this is to define the sixth as a > special [moleculetype] (even if it contains identical information) with a > different name, such that it can be restrained in the absence of restraints > on the others. See the logic here: > > http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_* > *restraints_out_of_bounds<http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds> > > -Justin > > -- > ==============================**========== > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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