RE: [gmx-users] Protein-Ligand Docking?

Just as Mark and Justin have said, this is up to you to define this question. The reason I said that, is you were asking "how do I know if my molecule is docked to the protein?". The first step to answering that question is defining what you mean by being docked. Once you have a definition, then

[gmx-users] Protein-Ligand Docking?

Hi 1. If any one know the related paper of protein-ligand docking using MD, please refer to to those papers. 2. from Justin => "we often start with a protein-ligand complex for which we know the position and orientation of some inhibitor, usually from X-ray diffraction data. We test our model to

Re: [gmx-users] Protein-Ligand Docking?

Chih-Ying Lin wrote: HI Would you please give me an example of "definition" of DOCKed? That's your job ;-) Try searching the web or literature. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Protein-Ligand Docking?

Chih-Ying Lin wrote: HI Would you please give me an example of "definition" of DOCKed? You have to have some criteria to start with. When we do true docking, we often start with a protein-ligand complex for which we know the position and orientation of some inhibitor, usually from X-ray d

[gmx-users] Protein-Ligand Docking?

HI Would you please give me an example of "definition" of DOCKed? Thank you Lin First step, define what you mean by being "DOCKed". Second step, determine if those conditions are meet by your protein and ligand. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology an

Re: [gmx-users] Pressure coupling and cut-off

Yanmei Song wrote: Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10n

Re: [gmx-users] -np switch

Payman Pirzadeh wrote: Hello, When we use ‘mdrun’ or ‘grompp’ with the switch ‘-np’ we specify the number of nodes according to the manual. Does it mean if the nodes have 2 processors, then the simulation will be run on 4 CPUs or in –np we should specify 4 instead of 2? As of version 4.

Re: [gmx-users] -np switch

Payman Pirzadeh wrote: Hello, When we use ‘mdrun’ or ‘grompp’ with the switch ‘-np’ we specify the number of nodes according to the manual. Does it mean if the nodes have 2 processors, then the simulation will be run on 4 CPUs or in –np we should specify 4 instead of 2? Tell GROMACS the num

[gmx-users] -np switch

Hello, When we use 'mdrun' or 'grompp' with the switch '-np' we specify the number of nodes according to the manual. Does it mean if the nodes have 2 processors, then the simulation will be run on 4 CPUs or in -np we should specify 4 instead of 2? Payman _

Re: [gmx-users] Pressure coupling and cut-off

Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10ns. nstcomm

Re: [gmx-users] Pressure coupling and cut-off

Yanmei Song wrote: Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t

[gmx-users] Pressure coupling and cut-off

Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 Pcoupl

Re: [gmx-users] Constraints specified in .mdp as well as in .top files

Vishwanath Dalvi wrote: Hi! I have a question about a possible redundancy/conflict in specifying bond-constraints. I have in my simulation (among other things) a number of bonds - some of which are harmonic while some are rigid (or constrained). I specify the bonds in the .itp (or ultimate

Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

Harry Saavedra wrote: Dear All, I run a test molecule insertion simulation using Gromacs 4.0.3. All the molecules of the system work with two energy groups (two tabulated potentials), and every atom belongs to a different charge group; but Gromacs shows an error message: > grompp... > mdr

Re: [gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472

intra\sa175950 wrote: Hi all For a research project, I need to know how gromacs work/scale (especially gmx 4.0.4) in SGI ALTIX ICE 8200 EX machine cluster with Intel Quad-Core E5472. I want to simulate a molecular system (with 14 amino acid peptide +/- 5000 water molecules) in explicit co

[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

Dear All, I run a test molecule insertion simulation using Gromacs 4.0.3. All the molecules of the system work with two energy groups (two tabulated potentials), and every atom belongs to a different charge group; but Gromacs shows an error message: > grompp... > mdrun ... Program mdrun, VE

[gmx-users] Coulomb energies for a charge seperated species

Dear Gromacs Users, I am simulating a system that consists of a tryptophan linked to a thymine dimer (two thymine bases stacked together) and am interested in how the configurational properties of neutral tryptophan linked to neutral thymine compares with tryptophan cation linked to thymine an

[gmx-users] Constraints specified in .mdp as well as in .top files

Hi! I have a question about a possible redundancy/conflict in specifying bond-constraints. I have in my simulation (among other things) a number of bonds - some of which are harmonic while some are rigid (or constrained). I specify the bonds in the .itp (or ultimately in the .top) files as fol

Re: [gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472

intra\sa175950 wrote: Hi all For a research project, I need to know how gromacs work/scale (especially gmx 4.0.4) in SGI ALTIX ICE 8200 EX machine cluster with Intel Quad-Core E5472. I want to simulate a molecular system (with 14 amino acid peptide +/- 5000 water molecules) in explicit

[gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472

Hi all For a research project, I need to know how gromacs work/scale (especially gmx 4.0.4) in SGI ALTIX ICE 8200 EX machine cluster with Intel Quad-Core E5472. I want to simulate a molecular system (with 14 amino acid peptide +/- 5000 water molecules) in explicit conditions with PME and 32 -

Re: [gmx-users] How to set up dihedrals

Thomas Schlesier wrote: Dear all, i'm making a .rtp for a sugar for the OPLS-AA force-field. To start i made a topology with the PRODRG server, so i have a list with all bonds, angles and dihedrals, but the problem is, that i'm missing the unpolar hydrogens. How to set up the bonds and angles ent

Re: [gmx-users] Protein is not at the centre of octahedron box

sukesh chandra gain wrote: Dear All, I am doing a simulation for ligand-enzyme complex in a octahedron box. I have mentioned -c with editconf, but after energy minimization the protein is placed at the top of the box. Could you please suggest me how could I keep the protein at the centre of

[gmx-users] Protein is not at the centre of octahedron box

Dear All, I am doing a simulation for ligand-enzyme complex in a octahedron box. I have mentioned -c with editconf, but after energy minimization the protein is placed at the top of the box. Could you please suggest me how could I keep the protein at the centre of the octahedron box? Here are

Re: [gmx-users] problem regarding dna-protein simulation

nitu sharma wrote: Hello mark thanks for your suggestion . but i already did these these things which u suggest . There is nothing about nucleic acid database as i mentioned in my previous mail . I have solved the problem regarding aminoacid hydrogen database problem but it not

[gmx-users] problem regarding dna-protein simulation

Hello mark thanks for your suggestion . but i already did these these things which u suggest . There is nothing about nucleic acid database as i mentioned in my previous mail . I have solved the problem regarding aminoacid hydrogen database problem but it not valid in case of nucleic a

[gmx-users] How to set up dihedrals

Dear all, i'm making a .rtp for a sugar for the OPLS-AA force-field. To start i made a topology with the PRODRG server, so i have a list with all bonds, angles and dihedrals, but the problem is, that i'm missing the unpolar hydrogens. How to set up the bonds and angles entrys is no problem, but wit

Re: [gmx-users] How to remove water from lipid bilayer core

Hello Anirban, Greetings from Pawan. You can find the scripts in this webiste : http://wiki.gromacs.org/index.php/Membrane_Simulations Regards, Pawan On Thu, May 14, 2009 at 3:01 PM, Anirban Ghosh wrote: > Hi ALL, > > I have a built a system of protein embeded in lipid bilayer and solvated it >

[gmx-users] How to remove water from lipid bilayer core

Hi ALL, I have a built a system of protein embeded in lipid bilayer and solvated it according to the GROMACS membrane simulation tutorial. I want to delete a few water molecules that are there in the hydrophobic core of the bilayer. I deleted them manually from the .gro file and corrected the a

Re: [gmx-users] problem in simulation of dna-protein complex

nitu sharma wrote: Dear all , I am doing simulation of DNA-protein complex. Is anybody have idea about .hdb of DNA becoz in mannual nothing is wrritten about DNA hydrogen database .I have edited The database like this- ADE 9 2 6 H5* C5* C4* O

[gmx-users] problem in simulation of dna-protein complex

Dear all , I am doing simulation of DNA-protein complex. Is anybody have idea about .hdb of DNA becoz in mannual nothing is wrritten about DNA hydrogen database .I have edited The database like this- ADE 9 2 6 H5* C5* C4* O5* 1 5 H4* C4*

Re: [gmx-users] Regarding the broken compiler gcc 4.1.x

On Thu, 2009-05-14 at 12:13 +0530, rashmi_c...@iitb.ac.in wrote: > Dear gmxusers, > > The warning on the GROMACS download page says : > > WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These > compilers come with recent Linux distrubutions like Fedora 5/6 etc. > > > So I i

Re: [gmx-users] Where are the good tutorials?

Casey, Could you expand your criticism? You must have found the tutorials section on the wiki. Then please note the specific points you dislike about the tutorials there (especially the beginners) and provide some ideas you would think improve them. To my opinion, a beginners tutorial provides a

[gmx-users] Regarding the broken compiler gcc 4.1.x

Dear gmxusers, The warning on the GROMACS download page says : WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. So I installed CentOS 4.3 with gcc 3.4.5 and Fedora 10 with gcc 4.3.2 on two different ma