Hi,
Do you have any idea how to steered several atoms towards a target atom in AMBER?
Set collective variable file (cv_file) in &smd namelist.
How to merge two lammps data file?
04 June 2024 3,478 2 View
Hi Folks, There is an urgent need to relocate a beehive (pic attached) from an ongoing construction site in Saudi Arabia. As is evident from the pic, it happens to be on a coral bed above the...
17 February 2024 277 5 View
The exploration of this question aims to shed light on potential challenges and risks associated with the convergence of these factors, emphasizing the importance of media literacy in navigating...
10 January 2024 2,464 0 View
Any suggestion would be highly appreciated.
16 November 2023 3,002 0 View
Is it correct to treat RAW264.7 mice macrophage cell line with recombinant Human Macrophage Migration Inhibitory Factor (MIF). Will there be any species incompatibility related unwanted effect on...
12 November 2023 1,534 1 View
If there are two simulation, one is atomistic and the other coarse-grained, so what should be the strain rate for those simulation? same or different? Any suggestions will be highly...
27 October 2023 337 0 View
Lammps command: If you pull in a particular direction, using "fix 4 all deform 100 z scale 3 units box", how to calculate the strain rate? Is it through back calculation?
15 October 2023 3,000 3 View
The experiment was done in an augmented block design with 183 genotypes whose data is not replicated within environment but the checks were replicated within each environment.
21 August 2023 2,726 2 View
is there any accessible document that provides a detail of the stratigraphy with age and environment of deposition encountered in well Ile Saint Marie-1 drilled in the eastern coast of Madagascar?
17 July 2023 2,923 0 View
Hi Folks, The attachments are 5 bat calls, recorded via Anabat detector, from Umluj, Tabuk Province, Kingdom of Saudi Arabia. I analyzed them using Anabat Insight's BatClassify Plugin. On...
09 September 2022 8,555 2 View
Hello, I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page: http://www.probechem.com/products_PRG-A01.html I used the guide made by Michael...
17 July 2024 3,472 3 View
I have been able to assign the CHARMM forcefield to my ligand i.e. acetyl coenzyme A but not the amber forcefield. I want to run amber forcefield and the parameterization of ligand is failing. I...
15 July 2024 7,323 1 View
Hello, I am doing ONIOM QM/MM energy calculation. I am adding explicit solvent. My input keywords is below: # oniom(m06/6-31g(d,p):amber=hardfirst) scrf=(iefpcm,read,oniompcm=x) nosymm...
04 June 2024 5,825 1 View
Hi, I'm new to QM/MM calculations, and I've recently started a calculation for a laccase enzyme containing 4 Cu ions. Following the Ambertools MCPB.py tutorial, I've created these files:...
30 May 2024 7,237 0 View
Good morning, I am running some Steered molecular dynamics in Amber 22 and want to set some restraints in the z-axis so as to imply certain distances from my ligand to its substrate. My goal is...
27 May 2024 7,082 1 View
Dear Experts, I am currently conducting a Molecular Dynamics (MD) simulation using the NAMD package to observe the formation of a two-phase system between glucose, acetonitrile, and water. To...
26 May 2024 5,711 2 View
I have already tried AMBER and other force fields. The problem is with topology file creation. As there is no crystal structure or even a similar structure. So, I have to predict the structure...
19 May 2024 4,082 1 View
I am measuring primary aromatic amines by UV-VIS and using the NEDA solution as my coupling reagent. The method says that the reagent needs to be made fresh every day. However, the solution is...
29 February 2024 6,575 2 View
Hello, I have a question regarding GAFF force-field. Is GAFF use lennard Jones 12-6 or lennard jones 9-6? I checked amber website for that couldn't get a direct answer. I know 9-6 lennard...
07 February 2024 2,590 3 View
I am doing md simulation of HDAC11 protein with prospective ligands. I have completed molecular dynamics production run. But whenever I am doing MMPBSA.py assay, it is showing following...
18 January 2024 6,804 1 View