Re: [gmx-users] Gromacs setup on dual core machine

Hello Ricardo Did you install with the sources ? (make install) ? Go to the folder where you ran this command and run "make uninstall" Matheus Fazian Ige Gondo Departamento de Física e Biofísica Instituto de Biociências Unesp - Botucatu - SP [EMAIL PROTECTED] +55 (14) 3811-6254 On Tue, Mar 11, 2

Re: [gmx-users] parameter on Energy Minimization

Quoting Liu Shiyong <[EMAIL PROTECTED]>: > Thanks Mark and Justin. > > I did experiment with the following editconf.It works. Thanks. > > editconf -f ${file}.gro -o ${file}_box.gro -d 0.75 -bt cubic > > By the way, how to select box size automatically ? I just gave an > arbitrary

Re: [gmx-users] parameter on Energy Minimization

Thanks Mark and Justin. I did experiment with the following editconf.It works. Thanks. editconf -f ${file}.gro -o ${file}_box.gro -d 0.75 -bt cubic By the way, how to select box size automatically ? I just gave an arbitrary number: 0.75 Another question is how to get the str

Re: Re[2]: [gmx-users] size of the system

> It seems my answer to Berk was processes by the system > in a wrong way. > >> guess this procedure should work, so this might be a bug. >> But you are making things much more complicated than needed. >> You can skip the first two steps and just use the -box option of genbox >> instead of -cp. >>

Re: [gmx-users] parameter on Energy Minimization

> Hi, > > I used a script given below for energy minimization of a native > protein-protein complex 1akj. > > I removed HETATMs and water molecules from the structure, and the > minimized > structure (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80. > Then I used rasmol to check the result. The li

Re: [gmx-users] Gromacs setup on dual core machine

Ricardo, you don't need to uninstall anithing. To run mpi jobs you only need, mdrun_mpi. ./configure (with your options) make mdrun make install-mdrun done. On Tue, Mar 11, 2008 at 1:55 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote: > > Kpiwara De X-nelo wrote: > Hello > You'll need FFTW (fftw

[gmx-users] pdb2gmx error

Hi, I have used gromacs simulations before for protein-small molecule. I have not seen this following error previously. All of a sudden, when I run pdb2gmx on my protein file, I get this error below. I did not make any chages to the way my machine is set up or other gromacs related settings, so I

Re: [gmx-users] parameter on Energy Minimization

Quoting Liu Shiyong <[EMAIL PROTECTED]>: > Hi, > > I used a script given below for energy minimization of a native > protein-protein complex 1akj. > > I removed HETATMs and water molecules from the structure, and the minimized > structure (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80. > Then I

Re: Re[2]: [gmx-users] size of the system

The Ubuntu package I had for version 3.3.1 was broken, although it manifested itself in different ways. I would suggest obtaining the source code and re-compiling Gromacs. -Justin Quoting "V.V. Chaban" <[EMAIL PROTECTED]>: > JAL> the gcc 4.1.x compilers produce a broken product. > > It seems e

Re[2]: [gmx-users] size of the system

It seems my answer to Berk was processes by the system in a wrong way. > guess this procedure should work, so this might be a bug. > But you are making things much more complicated than needed. > You can skip the first two steps and just use the -box option of genbox > instead of -cp. > > Berk.

[gmx-users] parameter on Energy Minimization

Hi, I used a script given below for energy minimization of a native protein-protein complex 1akj. I removed HETATMs and water molecules from the structure, and the minimized structure (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80. Then I used rasmol to check the result. The ligand is ran away

Re[2]: [gmx-users] size of the system

JAL> the gcc 4.1.x compilers produce a broken product. It seems everything is OK with genbox (ver 3.1 and 3.3). When doing the same with any protein.pdb (+water from spc216.pdb) it works. The problem occurs only when I deal with any pure solvent. Vitaly __

Re[2]: [gmx-users] size of the system

> I guess this procedure should work, so this might be a bug. But you are making things much more complicated than needed. You can skip the first two steps and just use the -box option of genbox instead of -cp. Berk. OK.  genbox -cs spc216.pdb -box 3 3 3. It outputs:       Opti

Re: [gmx-users] Gromacs setup on dual core machine

Kpiwara De X-nelo wrote: Hello You'll need FFTW (fftw.org ) LAM/MPI (lam-mpi.org ) and gromacs sources Download the 3 packages start with the Lam/MPI (configure , make , make install) Then fftw (the 2.1.5 version is needed, the 3.2 supports it but is still

Re: [gmx-users] size of the system

Quoting "V.V. Chaban" <[EMAIL PROTECTED]>: > Dear Colleagues, > > I've got a novice question as for GROMACS. For example, I need a system > of 500 water molecules. Initially, I've spc216.pdb. Then I try: > pdb2gmx -f spc216.pdb -o conf.pdb > editconf -f conf.pdb -o box.pdb -d 0.7 > genbox -cp box.

[gmx-users] size of the system

Dear Colleagues, I've got a novice question as for GROMACS. For example, I need a system of 500 water molecules. Initially, I've spc216.pdb. Then I try: pdb2gmx -f spc216.pdb -o conf.pdb editconf -f conf.pdb -o box.pdb -d 0.7 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top The utility outp

Re: [gmx-users] ligand-protein interaction using gromacs

Regarding amb2gmx.pl, it should work for converting whole systems from Amber, but this may depend on the box geometry you are using. In particular I think it is OK with cubic boxes but not some of the more fancy geometries. The other option is just to convert your protein+ligand and solvate using g

RE: [gmx-users] Avoiding parameterization step

> Hi Gerrit, > > Thank you very much for your response. I am at the moment interested in > doing conformational search. > Is there any good paper that explain nicely about doing the charge > distribution calculation? See http://wiki.gromacs.org/index.php/Parameterization Mark __

Re: [gmx-users] Calculation of Dihedral angles

Quoting Anirban Ghosh <[EMAIL PROTECTED]>: > Hi All, > I have a wild type protein and a mutant. I want to see whether there is any > dihedral transitions occuring in the mutant. How should I calculate these > dihedral properties?I used g_angle command, but it gave the error: Well, what command di

[gmx-users] Calculation of Dihedral angles

Hi All, I have a wild type protein and a mutant. I want to see whether there is any dihedral transitions occuring in the mutant. How should I calculate these dihedral properties?I used g_angle command, but it gave the error: Fatal error: Can only do transition, fraction or correlation on dihedra

Re: [gmx-users] Ki estimation

You can't compare a Ki directly from the MD AFAIK. What you could do is, computing the free energy difference between two ligands and compare it to the difference in Ki (which actually is closely related to the famous Kd), if that helps you Regards Maik Goette, Dipl. Biol. Max Planck Institut

Re: [gmx-users] Avoiding parameterization step

Thank you very much for your response. I am at the moment interested in doing conformational search. Using freeze groups in combination with conformational search does not seem optimal... Is there any good paper that explain nicely about doing the charge distribution calculation? Y

RE: [gmx-users] Avoiding parameterization step

Hi Gerrit, Thank you very much for your response. I am at the moment interested in doing conformational search. Is there any good paper that explain nicely about doing the charge distribution calculation? With regards, Abu > Date: Tue, 11

Re: [gmx-users] ligand-protein interaction using gromacs

Quoting #NGUYEN CONG TRI# <[EMAIL PROTECTED]>: > Dear all, > > I'm trying to study the interaction between NADH and a protein. And because > the parameters for NADH have been developed in amber99 and amber94 force > fields, so I just used the contributed parameter files for my simulation. The > co

Re: [gmx-users] Error of atomtype not found

Quoting s lal badshah <[EMAIL PROTECTED]>: > Dear Gromacs Users, > The file which I used for ions.itp is, now I change oplsa_405 by Na but it > give again the error > Fatal error: > Atomtype 'Na' not found! > Please guide me. That is because 'Na' is the nomenclature used by ffgmx. If you want OP

Re: [gmx-users] Avoiding parameterization step

Hi All User, I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD simulation. Depends on what you want to do. You most likely would still need the charge distribution, which is the most difficult part of the parametrization part usually

Re: [gmx-users] Ki estimation

Unless you have multiple events of binding and unbinding you cannot directly calculate the Ki from EM or MD. You can use approximated methods, e.g. LIE and MM/PBSA (with MD) or LIECE (for a static structure). All of these depend on the choice of empirical parameters. Best regards, Ran. V. Tanchu

[gmx-users] Avoiding parameterization step

Hi All User, I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD simulation. With regards, Abu _ Free games, great prizes - get gaming at Gamesbox. http://www.searchg

[gmx-users] Avoiding parameterization step

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[gmx-users] Avoiding parameterization step

Hi All User, I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD simulation. With regards, Abu _ Share what Santa brought you https://www.mycooluncool.com_

[gmx-users] Avoiding parameterization step

Hi All User, I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD simulation. With regards, Abu _ Who's friends with who and co-starred in what? http://www.searchgamesb