Seketoulie Keretsu

8 Questions 10 Answers 0 Followers

Questions related from Seketoulie Keretsu

Command to select starting and ending frames in g_mmpbsa binding energy calculation. Any suggestions?

I have a 30ns protein-ligand simulation trajectory from Gromacs. I would like to use the last 5ns (i.e 25-30 ns) of the trajectory for binding energy calculation. As mentioned in the g_mmpbasa...

01 January 2019 2,674 3 View

What are some journals that publish good Molecular Dynamics Simulation papers without experimental validation?

where can i find good molecular dynamics simulations papers without experimental (wet lab) counterparts. This is for computational biologist without a wet lab set up. Given that most journals...

12 December 2018 8,449 10 View

When i tied visualizing the 3D similarity between two protein in pymol. why do i get the yellow lines connecting pair of atoms??

I used the "align" command in pymol to visualize two proteins having >31% sequence similarity: command: align protein1, Protein2, object=mynewobj, cycles=1 I got the alignment but there are...

06 June 2018 8,514 3 View

Gromacs 5.0.7 installation: gromacs commands executes only after running "source" command. what could be the reason?

I just installed the gromacs-5.0.7 on linux CentOS. Commands are working as expected. However, unless I give the " source /user/local/gromacs/bin/GMXRC" once the shell does not recognize the...

05 May 2018 929 3 View

Can 3D-QSAR techniques be applied to series of inhibitors that forms covalent interaction with active site residue?

I have a series of irreversible covalent kinase inhibitors. Data shows the covalent interaction of inhibitor with active site residue play crucial role in activity value. Figure shows the most...

03 March 2018 1,125 1 View

Gromacs tutorial: preparation and simulation of a simple membrane protein available?

Dear Gromacs Experts I am currently doing the gromacs tutorial for simulation of membrane protein (KALP15 in DPPC by Justin A. Lemkul). I came across several challenges most of which I could...

01 January 2018 6,240 7 View

Amber Vs Gromacs: what's your take?

Ignoring the fact that one of them is commercial and one is not both Amber and Gromacs are very resourceful ( packages and tools ). I have tried tutorial of both amber and gromacs and I find...

01 January 2018 8,995 3 View

How would you explain Umbrella sampling in Molecular Dynamics?

How would you break down Umbrella sampling to a newbie or to someone not from quantitative studies. Is there a good analogy to understand this? I am using gromacs for simulation. Opinions and...

01 January 2018 822 8 View