Re: [gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Tsjerk Wassenaar
Hi Atila, > ; Include chain topologies > #include "complex_Protein_chain_A.itp" > #include "complex_DNA_chain_B.itp" > > ; Include Position restraint file > #ifdef POSRES > #include "posre_Protein_chain_A.itp" > > ; Include Position restraint file > #ifdef POSRES > #include "posre_Protein_chain_B.

Re: [gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Justin A. Lemkul
Atila Petrosian wrote: Dear Justin thanks for your attention I deleted posre.itp file which pdb2gmx was created (containing all solute).I made a posre.itp (containing only protein) by genrestr. now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true? Assuming you have

Re: [gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Mark Abraham
On 27/10/2011 12:28 AM, Atila Petrosian wrote: Dear Mark thanks for your reply you said "if pdb2gmx is able to treat the whole system in one pass, then it will write such position restraint files automatically" in my system, what pdb2gmx includes are in below: ; Include forcefield parameter

[gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Atila Petrosian
Dear Justin thanks for your attention I deleted posre.itp file which pdb2gmx was created (containing all solute).I made a posre.itp (containing only protein) by genrestr. now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true? -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Justin A. Lemkul
Atila Petrosian wrote: I want to use define = -DPOSRES_Protein_chain_A for step 1. is it true? Not per the topology you posted earlier. Your only option (at this point) for restraining the protein is -DPOSRES, which restrains all the chains. If you want to restrain parts of your stru

[gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Atila Petrosian
I want to use define = -DPOSRES_Protein_chain_A for step 1. is it true? -- 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

[gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Atila Petrosian
Dear Mark thanks for your reply you said "if pdb2gmx is able to treat the whole system in one pass, then it will write such position restraint files automatically" in my system, what pdb2gmx includes are in below: ; Include forcefield parameters #include "amber03.ff/forcefield.itp" ; Include c

Re: [gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Mark Abraham
On 26/10/2011 11:24 PM, Atila Petrosian wrote: Dear all my system contains protein + ligand+ water molecules. protein + ligand = solute water molecules = solvent I want to do minimization energy in 3 steps : step 1) on protein only step 2) on all solute (protein + ligand) step 3) on all sy

[gmx-users] position restrained minimization on the one part of a system

2011-10-26 Thread Atila Petrosian
Dear all my system contains protein + ligand+ water molecules. protein + ligand = solute water molecules = solvent I want to do minimization energy in 3 steps : step 1) on protein only step 2) on all solute (protein + ligand) step 3) on all system should I use position restrained minimizati