hello i have a query is it anyone use the pyred server for amber ? i have query regardind
i am unable to interpret why its increases in start as shown in figure
11 August 2024 2,179 1 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
Hi all, I was just wondering if anyone has experience with multiplexing a mouse monoclonal primary and a rat primary. I'm trying to multiplex by incubating them in the same well but was told by a...
06 August 2024 9,710 1 View
A Markov-like Model for Patient Progression" Markov Chain Monte Carlo (MCMC) Markov Chain Monte Carlo (MCMC) is a powerful computational technique used to draw samples from a probability...
05 August 2024 10,079 0 View
I am currently working on modeling FCC catalyst regeneration and have come across a point of uncertainty that I hope you can assist me with. In my previous models, I have utilized lumped kinetics...
30 July 2024 6,137 0 View
I'm a PhD Student. From Northwest Agriculture and Forestry University China. My Problem is this I start my work on bhlh79 transcription factor gene. I do my Y2H 5 time but the colonies appear on...
30 July 2024 1,412 8 View
Kao's panel cointegration tests , is there anyone willing to explain me the eviews-9 output for the Kao's panel cointegration tests?
23 July 2024 5,051 4 View
Please inform me about the International Conference on Plant Molecular Biology, or Plant Biology, scheduled for December 2024, January/February, or March 2025.
14 July 2024 3,120 7 View
need to know protocol for photoplate creation, styles, etc
11 July 2024 8,321 2 View
How can anyone develop a theoretical framework that successfully unifies general relativity and quantum mechanics? how this new theory should accurately describe gravitational interactions at...
10 July 2024 5,040 8 View
To help enchancing patients flow and service efficiency
18 July 2024 482 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
Preprint servers play a valuable role in the scientific publishing workflow by accelerating the sharing of research, promoting openness and transparency, and diversifying the publication...
01 July 2024 4,022 2 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
I've used Origin 2024 trial for 6 month. Now the licence is expired, I'm using Origin 2016 of which the licence is available for me. But, error message "The server application, source file, or...
02 June 2024 7,465 1 View
Previously I have used GlyProt to add carbohydrate chains with my modelled protein, but the server is not working now. Is there any alternative tool for modeling glycosylated protein?
01 June 2024 894 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
I would like to know other researchers opinion about their preferred preprint servers/platforms
28 May 2024 8,291 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