Hi All,
Can any one please tell me how I can apply "random incremental pulse search" (RIPS) for side chains of amino acids interacting with certain ligand. Which software (with link to the software) to use and steps to do that.
Best,
Hi All, I'm trying to prepare qm/mm files for a ligand bound to an enzyme, I followed the tutorial of "vmd" and "namd", but it still reports an error in qm calculations. Any idea please? Best,
08 September 2018 890 0 View
Can anyone please help in finding the Fourier transform of the distance equation? The distance equation is: (Z2-Z1)2+(Y2-Y1)2+(X2-X1)2=D2 X1,Y1,Z1 are the coordinates of the first point. X2,Y2,Z2...
04 May 2017 262 3 View
Hi all, I need simple executable to perform steepest descent minimization for protein structure (pdb), with instruction how to do it? Thanks,
10 November 2016 7,960 1 View
Hi All, 1-How Can I call "NAMD" (Molecular Dynamics software) from *.bat file on windows. Usually, I use cmd.exe to run NAMD by the following command: namd2 +p12 input.conf > output.log. I...
09 October 2016 7,593 0 View
Can anyone please explain if there is any software to produce coarse-grained 3D structure for RNA and DNA?, I'm interested in the model of five key atomic positions in each nucleotide: two beads...
05 June 2016 3,401 5 View
In Running MD simulations of some enzymes containing phosphoserine, where can we find forcefields for phosphoserine to use with "NAMD". Thanks,
05 June 2015 7,137 6 View
We use different ensembles in MD, which one is preferred to use?
02 March 2015 7,434 14 View
With NAMD, Where can we find standard config files for minimization, heating, equilibration, and production for all types of ensembles (NVE,NVT,& NPT)?
02 March 2015 6,214 4 View
In Molecular dynamics (NVE ensemble), is energy drift of about +5 Kcal/mol.ns acceptable?
02 March 2015 3,822 2 View
How can we solve energy drift problem in NVE (constant energy, constant volume, and constant number of particles) ensemble in Molecular Dynamics?
02 March 2015 1,369 3 View
Hello experts, Does anyone know any free software about retention index prediction ?
08 August 2024 7,403 2 View
Hello What should be done to separate and identify organic acids in HPC when their RetTime is the same?Like oxalic acid with Propanoic Acid.or acids that have a very close RetTime.
07 August 2024 8,782 3 View
Dear readers, Thanks for your attention. I am wondering about the health economic problem of quantifying the value of interventions which a) prevent, b) improve symptom profile and c) ultimately...
05 August 2024 3,246 1 View
why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...
03 August 2024 3,589 3 View
I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...
03 August 2024 1,370 1 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
I am attempting to conjugate PEG to an amino acid at the C-terminus, for the purposes of producing nanoparticles. I have been told that PEG modified with amine groups can be used for this purpose,...
31 July 2024 2,033 1 View
Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer
30 July 2024 3,354 1 View
Hi, researchers, Is it possible to use a safer acid instead of monochloroacetic acid to convert bacterial cellulose to carboxymethyl cellulose?
29 July 2024 4,570 0 View
I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...
28 July 2024 2,979 1 View