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,
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
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...
08 September 2016 1,808 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
The paper in question is "Interpolation of Nitrogen Fertilizer Use in Canada from Fertilizer Use Surveys". This paper was very recently published by Agronomy (MDPI). Agronomy has, in the last day...
07 August 2024 9,934 3 View
Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out
07 August 2024 6,066 0 View
The first pdf file I uploaded had an error. So I uploaded an updated, corrected pdf of that paper with a different pdf name. I dpon't want the old copy to be download or read.
07 August 2024 9,508 1 View
Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...
06 August 2024 4,953 0 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
Dear Researchers Kindly share JCPDS 65-7246 file Thanks in advance
04 August 2024 5,613 1 View
Hi everyone I need a file with a dirty and clean potato image
04 August 2024 7,199 4 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