I want to attach methyl forming covalent bond with Oxygen of Guanine in DNA. How can we do it using Avogadro ?
Thanks
Hi all, I am working on a MD simulation of a membrane protein inside the POPC bilayer using namd. At first, I ran a short constrained dynamics by applying harmonic constraints to both...
05 June 2019 7,435 4 View
Hi everyone, My system is a dimer. During the MD simulation, I can see a strong hydrogen bond formed between two lysine residues which are at the side chains of two peptides. But, the issue is...
04 May 2019 6,105 5 View
Hi everyone, While using the PDB reader of charmm-gui for my membrane protein system which is a dimer, I got stuck at PDB manipulation option. It gives me option regarding...
04 May 2019 2,487 3 View
Can anyone please suggest me review articles/papers/books/links on understanding protein-lipid interactions through Molecular Dynamics simulation ? Thanks
01 February 2018 4,939 3 View
Is there any standard value like two non-bonded residues or atoms are considered to form a contact if their distance is less than ? I usually use like 1.4 nm for short range non-bonded LJ cut-off...
01 February 2018 9,846 4 View
Are there any scripts or tools available in python to plot the running average of the data similar to as shown in the figure attached? Thanks
31 December 2017 2,525 4 View
I want to rotate a specific residue (say "resid 7 and resname MET") by 180 degrees around x-axis and save the coordinates. Can it be done using VMD's TK Console ?
31 December 2017 7,579 7 View
The characteristic frequency of thermal motion is around 7E12 Hz at room temperature (300K), but from that information how can we conclude that the bonds are hard; they don't vibrate !!
31 December 2017 6,084 2 View
I want to measure the tilt of helix with the normal of bilayer. My system is basically a dimer with two helices. Since using sidechain atom relative to the axis is optional, I simply defined...
31 December 2017 730 3 View
Are there any gromacs or other tools available to look for or find the number of protein-lipid contacts during Molecular Dynamics simulation of membrane protein ?
11 December 2017 2,812 3 View
I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?
11 August 2024 5,138 1 View
After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...
08 August 2024 1,668 3 View
I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you
08 August 2024 4,733 2 View
Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...
07 August 2024 8,414 2 View
Greetings When one is to perform Simulation or modelling of Pyrolysis of Biomass Waste materials using Aspen Plus software, and one has both the macromolecules breakdown (Cellulose, Lignin and...
06 August 2024 5,023 1 View
I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...
05 August 2024 9,059 3 View
Hello. I am working on ROS production of two systems: system A is cerium oxide and hydrogen peroxide, system B is cerium oxide nanoparticle, hydrogen peroxide and potassium bromide. I did some...
04 August 2024 5,974 3 View
Why BaO (s) + H2O(l) ---> Ba 2+(aq) + 2 OH - (aq) if Oxygen loves owning all the electrons, why would it bind to hydrogen which competes with Oxygen for electron ownership more so than...
03 August 2024 5,392 1 View
I heard an explanation about something being a better proton acceptor or lone pair donor but that doesn't make sense. I couldn't explain in in terms of acid-base theory. The hand-waving way I saw...
03 August 2024 9,918 0 View
I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...
01 August 2024 2,079 0 View