I have a system of a protein co-complex which behaves like a polymerase. One of them recognises the binding site and other catalyses the reaction.
I am confused between ff14SB and PARMbsc1. What should I use ?
Dear Hindol,
For force field parameters you can use ff14SB for protein and PARMbsc1 force field is for Nucleotides(DNA and RNA).
It would help if you incorporated both the force field parameter.
Using the PARMbsc1 force field shows good agreement for the experimental results.
Please look amber-20 force field manual and especially "Molecular mechanics force fields".
Also, look at "https://www.youtube.com/watch?v=iQThYDiJs7c&ab_channel=CHARMM-GUI" choosing the force field paramter.
Hopefully, it will help.
Best Regards
Aashish
Can we measure the bulk composition of biomolecules present within an algal sample directly by placing its powdered form on a FT-IR spectroscopy stage? Or does it require a particular kind of...
30 January 2021 2,303 4 View
I want to plot the distribution curve of dipole moment as a function of angles between dipole vector and solid surface in the presence of external electric field. My system is consisting a...
17 January 2021 1,508 4 View
I need to dissolve 1.5gm of PVDF tablets (from Sigma ALdrich) in 25gm of n-n DiMethyl Acetamide (DMAc) solvent. I have stirred the solution for 2 hours using magnetic stirrer and it did not seem...
02 December 2020 1,777 3 View
I have a PEM cell dataset, and I want to plot the degradation curve or polarization curve using machine learning algorithms. How can I approach in this regard. I have to design an algorithm to do...
18 October 2020 7,909 2 View
07 October 2020 8,119 6 View
A particular gene (gene A) is reported to be downregulated in cancer cells as compared to the normal cells. How can you prove this with the help of PCR?
27 September 2020 5,292 4 View
Free toxicity prediction software based on genetic algorithm and deep learning of some training dataset #toxicity #Freesoftware #insilico #Deeplearning
30 August 2020 7,950 4 View
Currently I am using dpm particle tracking in Fluent to trace some particle .After the completion of the simulation, how can I obtain the concentration versus time curve at the outlet?
28 August 2020 9,962 3 View
I am looking for a new mixture template which is not in the data base of Ansys Fluent species transport model. How could I add new template?
25 August 2020 6,340 2 View
I am trying to compute the median duration of postpartum insusceptibility for one of my objectives. However, my values are much lower than the ones in the published report. Can you please help me...
10 May 2020 1,032 7 View
Hello all, I need help getting started building and analyzing a UTATU model. I have a survey ready with some questions but I had some confusions on UATAUT and on how to analyze the data. I will...
02 March 2021 9,271 1 View
Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...
01 March 2021 8,747 4 View
There is confusion regarding the submillimeter-wave range. Many papers specify its range from 300GHz but some also consider its range from 100GHz. If I design an antenna on 122ghz what would I...
01 March 2021 516 7 View
I have several question regarding the MOR; hope anyone help me better understand. 1- in CV using (KOH+MEOH) what is the indication of absence of the redox peaks? shouldn't they exist as a sign...
28 February 2021 4,851 8 View
I am trying to identify these 3 genes among some tomato cultivar collections and after aligning some sequences from NCBI, I couldn't find unique sequences to target for specific primers. There...
28 February 2021 606 3 View
When you use RIA, with a control the unknown sample with antibodies, you bare in mind the binding sites of the antibodies. However you still need to measure labelled antigen (radioactive) and not...
28 February 2021 2,133 3 View
28 February 2021 5,433 3 View
Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...
26 February 2021 5,029 2 View
I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...
23 February 2021 711 3 View
Hello Everyone, Hope you all are doing well. I'm trying to simulate a machine foundation in ABAQUS with a geo-cell reinforced soil bed. Im totally confused to which type of loading would be...
21 February 2021 4,388 3 View