14 Questions 44 Answers 0 Followers
Questions related from Radhika Geethu
Hi Friends, I want to calculate delocalization index between the atoms involved in hydrogen bonding. I have an output of AIM analysis using MORPHY software. But I don't know to evaluate it. So I...
13 October 2016 4,476 15 View
Hi Friends, I have done a molecular dynamics simulation of a DNA molecule for 100ns in Gromacs with amber force field. I expected a well stabilized system but I got structures with small...
07 September 2016 9,110 9 View
Hi Friends, As I wanted to do structural studies of amonafide with the DNA sequence D(CCTGGTCC):D(GGACCAGG), I have done MD simulation in Gromacs with the force field amber99sb ildn. This DNA...
02 September 2016 2,800 7 View
Dear Friends, I used auto dock vina to dock telomere with a ligand. As I don't know which guanine in the G-quadruplex could be much specific for that ligand, I have done blind docking. But the...
22 January 2016 3,533 12 View
Dear Friends, I have used the below command to get the EPR spectrum in gaussian 09. #B3LYP/LANL2DZ prop=epr nmr nosymm Iop(3/32=2) Iop(6/82=1) Now I want to plot the EPR spectrum from the output....
11 December 2015 6,854 10 View
I am doing NMR studies of DNA - drug interacted complexes theoretically. While trying to compare it with the experimental results I am facing some difficulties. I want to know when an atom can...
09 October 2015 7,667 7 View
Recently I have referred a journal in which 1,8 Naphthalimide derived drugs were active on the HeLa cell lines. I am doing simulation work of DNA-anticancer drug interaction. I want to know how to...
14 January 2015 760 4 View
I am dealing with DNA-drug interaction studies. For the simulation I am using amber 03 force field in GROMACS 4.5.5 . To parametrize the ligand Quercetin I am using antechamber. I am trying to...
25 October 2014 8,279 10 View
Hello Friends, I have created an itp file for a drug by using PRODRUG. After that I have changed the charge values of the file (Using DFT). Now it is necessary to change the charge groups too?...
23 October 2014 5,405 3 View
I am in need of a database with vibrational frequencies of DNA. Can any one help me?
31 May 2014 2,063 2 View
I am doing spectroscopic studies on drug - dna interaction (theoretically). I want to know the absorbance values in terms of wavelength in the UV-absorption studies for a comparison purpose. But I...
30 April 2014 5,419 17 View
I am doing Drug-DNA interaction studies theoretically. For comparison purposes I want to know the experimental values of absorption and emission spectra for the DNA.
25 April 2014 2,145 4 View
I am doing drug - DNA interaction studies. For that I am in need of pdb files for di, tetra, hexa and oligo nucleotides (NMR structures are preferential). I didn't get some of the sequence of...
10 March 2014 9,533 5 View
Is there any possibility to use this software for the whole optimized structure of DNA (including QM/MM) or is this only for QM?
25 November 2013 8,362 3 View