Re: [gmx-users] a new GROMACS simulation tool

I also would like to try 2013/10/23 Gloria Saracino > Dear Kevin, > I'm Gloria Saracino from the Center of Nanomedicine and Tissue Engineering > of the Hospital of Niguarda Ca' Granda in Milan, Italy. > > I'm interested into knowing more about this new web based toolas I use MD > everyday. >

Re: [gmx-users] Visualize Protein ligand complex

Don't you wanna try to use the VMD use vmd xxx.gro yyy.trr and then you could highlight your ligand 2013/6/27 Sainitin Donakonda > Hi, > > I simulated protein ligand complex for 20 ns now i want to visualize this > complex after simulation in pymol.To look ligand interactions with protein >

[gmx-users] Molecule in topology has atom numbers below and above natoms

Hello Everybody I'm running a production simulation of a kinase (after minimization and equilibration) and after concluded 20ns I got the following problem when I tryied to run g_rmsf "Fatal error: Molecule in topology has atom numbers below and above natoms (4005). You are probably trying to use

[gmx-users] node decomposition' problem

I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: "There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum ce

Re: [gmx-users] Rhamnose on 53a6

Have you tryed online servers as http://davapc1.bioch.dundee.ac.uk/prodrg/or the Acpype (with Amber)? 2012/6/11 Marc Gordon > Hello again fellow gromacs users. > > I am looking to model a glucose-rhamnose disaccharide using the 53a6 > forcefield. I wanted to take a look at the naming conventions

Re: [gmx-users] doubt about OpenMM

I have Python 2.6.5 2012/5/2 Martin Hoefling > Am 30.04.2012 19:32, schrieb Thales Kronenberger: > > Hey Folks, > > > SUDO_USER=laboratorio24 > > PWD=/home/laboratorio24/OpenMM4.0-Linux64/python > > File "setup.py", line 165 > > print "%s

[gmx-users] doubt about OpenMM

Hi I trying to install the OpenMM to so run gromacs using GPU, but when I set the locals variables and type: "sudo ./install.sh" It's says: SUDO_USER=laboratorio24 PWD=/home/laboratorio24/OpenMM4.0-Linux64/python File "setup.py", line 165 print "%s" % outputString ^ SyntaxErro

[gmx-users] Acpype doubts

I configure Amber1.5 and installed the Acpype compatible (the tests went pretty well) BUT when I tried to submit my own job by the line acpype -i proteinname.mol2 -c user i got the message: == = | ACPYPE