Re: [gmx-users] Position Restraints of one of the moleculetpye
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 fcxfcyfcz 11 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_boundshttp://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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
Re: [gmx-users] Position Restraints of one of the moleculetpye
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 fcxfcyfcz 11 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 -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
Re: [gmx-users] Position Restraints of one of the moleculetpye
On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul jalem...@vt.edu 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 fcxfcyfcz 11 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
[gmx-users] Position Restraints of one of the moleculetpye
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? Best, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
Re: [gmx-users] Position Restraints of one of the moleculetpye
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 -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
