Radhika Geethu

10 Questions 33 Answers 0 Followers

Questions related from Radhika Geethu

What is the reason for not getting a well stabillized DNA molecule in a molecular dynamics simulation?

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 9,052 9 View

What could be done to avoid the disruption in DNA during MD simulation?

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 2,748 7 View

Does docking of a telomere with a ligand is reliable using blind docking method?

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 3,475 12 View

How do I plot the EPR spectrum from the g09 output?

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 6,827 10 View

When can an atom be represented as shielding or deshielding in proton, nitrogen and Carbon NMR?

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 7,626 7 View

How do I get the DNA sequence from specific cell lines?

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 705 4 View

How do I get RESP charges from antechamber?

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 8,227 10 View

How to separate the charge groups in Gromacs?

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 5,356 3 View

What is the relationship between absorbance and oscillator strength?

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 5,359 17 View

Can anyone help me find pdb files of nucleotides?

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 9,494 5 View