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

I also would like to try 2013/10/23 Gloria Saracino glos...@yahoo.it 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

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 saigr...@gmail.com Hi, I simulated protein ligand complex for 20 ns now i want to visualize this complex after simulation in pymol.To look ligand interactions

[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

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 marcgrd...@gmail.com 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

Re: [gmx-users] doubt about OpenMM

I have Python 2.6.5 2012/5/2 Martin Hoefling martin.hoefl...@googlemail.com 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 % outputString

[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 ^ SyntaxError:

[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: == = |