Hello,
I am studying a system with the method GaMD in Amber. Can I calculate collective variables like ALPHARMSD, BETARMSD, etc. from the Plumed? And then reweight with the GaMD reweighting methods?
Are there any statistical methods to justify your sampling technique using SPSS or AMOS?
05 August 2024 9,153 4 View
A molecule shows the -11.6 kcal/mol and second one -8.0 kcal/mol so why molecule (A) revealed higher binding score. Please explain major factor involve in it.
21 July 2024 954 5 View
Dear All, I want to cut PDMS sheet with thickness of 0.8 mm to rectangular shape with Graphtec cutter plotter CE6000-40. What condition do you offer? Do you offer any kind of special speed or force?
25 June 2024 8,111 1 View
How can we prove the strong electronic interaction between the catalyst and carbon cloth support?
19 April 2024 9,216 0 View
Hlo Researchers Any one can tell me how to isolate or estimate bacteriocins from lactobacillus spp producing strains from MRS media ? 1) At which stage it will be more suitable for sample...
28 March 2024 1,498 0 View
I want to use the TriFECTa RNAi kit for transfection, but I dont know how much RNA and control transfection should I use.
12 March 2024 1,515 2 View
Spirituality means something that actually you are, but without senses and body. But without senses and boy, what is left? and what is reach of present scientific approach.
20 February 2024 3,601 3 View
The variables under study are of mixed orders of integration i.e., I(0) and I(1). I want to estimate the long-run relationship between variables therefore it is recommended to apply pooled mean...
17 February 2024 6,566 3 View
If a compound has a lot of oxygen moities in ligand, so the docking score will be increase? If it will increase then what is the reason behind it?
16 February 2024 2,160 4 View
In the attached image, D1 dummies are for interaction term of public debt for each state, and D2 is a single dummy for structural break of Fiscal Responsibility Legislation implementation year...
27 January 2024 8,387 3 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