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Questions related from Sichaib Zeineb
Hi, I have trajectories of a protein embedded in an explicit membrane and water environment. I would like to estimate lipid-protein interaction durations i.e., the average duration of the...
27 October 2019 5,459 3 View
Hi, I have a Gaussian cube file (.cube) that I obtained with gmx spatial. It represents the spatial density of cholesterol during a simulation (Protein in a membrane with explicit solvent). I...
22 April 2019 8,521 1 View
Hi, I have a Coarse-grained simulation of a dimer with 5 transmembrane helices for each monomer and I would like to calculate the tilt angle of each monomer with the respect to the membrane...
25 January 2019 10,005 2 View
Dear all, I would like to simulate a protein which is located in the Mitochondrial Outer Membrane (OMM). I was searching in the literature about lipid composition of this latter (in Mammals) but...
05 February 2018 5,213 2 View
Dear all, I'm performing virtual screening on a library of 150 compounds. I used Vina, I selected the best 20 compounds and I docked them with AutoDock. I also used another program (surflex) in...
03 December 2016 3,465 9 View
Dear all, I have 2 separate PDB files (2 monomers of the same dimer) and I want to put them in one PDB file (PDB file of my final dimer). I opened the 2 monomers on PYMOL, did a select all and...
18 May 2016 9,163 5 View
Dear all, I'm working on simulating a homodimer with its cofactors (hem, THG) and its substrate with GROMACS. Since my system is complex, I decided to start first with a monomere taking only...
12 May 2016 6,357 2 View
Hello, I have missing atoms and residues in my PDB file and I need to fix them in order to proceed with pdb2gmx (GROMACS). I used swissModel but the generating file is lacking the final residue in...
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