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 6,929 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 8,642 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 2,727 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 5,003 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 5,705 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 2,226 3 View
Is there any software which could mine data from downloaded research articles (pdf format) as per one's requirement?
09 October 2018 3,897 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 248 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 5,384 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 6,799 5 View
I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance
03 March 2021 3,568 1 View
I am at the beginner level in drug design and drug discovery, and I am interested to learn more about this field. Which books are highly recommended to start from and gives me all essential...
02 March 2021 8,437 2 View
I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...
01 March 2021 8,544 1 View
We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...
01 March 2021 3,355 3 View
I am a little confuse with the mechanism of solid lipid nanoparticles (SLNs). The main point of encapsulating drugs into SLNs is because some drugs have low solubility in water. Therefore, SLNs...
01 March 2021 3,703 3 View
Hello, I was just wondering how does a antibody have full intact antibody + half antibody? Is it because of the drug conjugation?
28 February 2021 1,577 1 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
Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...
25 February 2021 6,969 3 View
I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?
25 February 2021 9,761 1 View
I am learning how to use SPM for PET and PET-MR analysis, but I haven't found any great resources that explain how contrasts work. I have a series of PET images where our hypothesis argues that...
24 February 2021 1,534 2 View
