Drug-DNA Interactions: Intercalating Drugs
I'm getting following error while pdb2gmx: Residue 2 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in...
09 October 2019 7,089 2 View
I'm getting following error in Amber: > loadoff drug.lib Could not open file drug.lib: not found Could not open database: drug.lib Please help!!
06 July 2019 8,794 2 View
I'm getting following error while executing following command: antechamber -i drug.pdb -fi pdb -o drug_bcc.prep -fo prepi -c bcc -s 2 Error: cannot run "/home/anwesh/softwares/amber14/bin/sqm -O...
06 July 2019 2,904 2 View
I have a *.fasta file through nanopore sequencing (Min Ion) of approx ~250MB. I'm having problem in its analysis via MEGA Software due to large file size. I need to select a particular bacterial...
05 June 2019 5,160 6 View
I'm currently working on metallic ligands (transition metals/complexes as ligands). For their MD Simulation, how to generate topology for ligand, kindly help?
04 May 2019 5,849 1 View
I have completed molecular dynamics simulation of some drug-DNA complexes, now I need to perform QM/MM calculations on the system. Please tell me as to how to set up a QM/MM calculation in...
09 October 2018 2,699 3 View
Is there any software which could mine data from downloaded research articles (pdf format) as per one's requirement?
09 October 2018 4,057 5 View
Is there any methodology to increase the no of cores (for faster computations) being used in the command line for mmpbsa claculations: g_mmpbsa -f md_0_1.xtc -s md_0_1.tpr -n index.ndx -i...
06 July 2018 492 5 View
I am performing MD simulation for drug-DNA complex using GROMACS via AMBER force field. At following step, the program shows an error: gmx genion -s ions.tpr -o solvated.pdb -p topol.top -pname NA...
04 May 2018 5,543 2 View
Can someone let me know about what is and how to perform, Umbrella Sampling in Molecular Dynamics Simulations, performed via GROMACS?
04 May 2018 6,964 5 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
I am experimenting with cancer and non-cancer cells in a 12-well plate for 4 days with a seeding density 1*10^4/well, however, I noticed that the control group growth rate slows down on D3. Should...
07 August 2024 2,283 2 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
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
I work on MCF7 cell cell for anticaner purpose and I wa to do drug preperation the drug ( secondary metabolites extracted from Aspergillus) My question which solvent is better with these secodary...
03 August 2024 4,725 2 View
Hello, if you made a transwell assay where you incubate the cells with a nanoparticle-encapsulated drug and considering that in the oposite compartment you'll have both the free and encapsulte...
03 August 2024 2,730 1 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
I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...
30 July 2024 6,420 1 View
