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Questions related from Pallavi Agrawal
how can i form the schematic diagram of g quadruplex as shown in figure?
25 November 2023 1,893 1 View
how to plot binding energy residue with respect to residue number in mmpbsa? i have done mmpbsa for dna-ligand complex. i want to calculate binding energy for every residue. Thanks in advance.
28 October 2023 3,649 1 View
I have done md simulation of a dna g quadruplex that contains metal ion in the center but after md simulation the metal ion come out from the dna g quadruplex. Ihave done position restraining and...
10 August 2023 1,644 0 View
i have done md simulation with gromacs software but when i check the trajectories with vmd their is a break in dna strand even after repeated simulation with ligand? what will be the possible...
28 March 2023 5,186 7 View
I am doing umbrella sampling using Justin Gromacs tutorial for DNA ligand complex. I am not able to understand how to make tpr-files.dat and pullf-files.dat. I manually paste umbrella.tpr file and...
17 October 2022 4,975 7 View
I have done MD simulation of DNA alone and complex, but the rmsd of the complex is much greater than alone DNA. What could be the possible reason for this? i have give centring command before...
27 September 2021 7,667 7 View
I have done PCA analysis of DNA ligand complex But it gives error diagonalizing segmentation fault core dumped. with this command- gmx covar -s ref.pdb -f md1_backbone.xtc
14 September 2021 7,552 3 View
I am using Haddock 2.4 to check docking parameters between DNA and ligand . My DNA file contain Na ion and I format it as given in Haddock library but it still gives the error - "Error in PDB...
16 June 2021 1,800 1 View
I have done md simulation using following commands- what is the meaning of this warning, it it harmful, hI attached e warning image and nvt.mdp in which I have done few changes gmx Add...
03 June 2021 286 0 View
I am doing DNA ligand complex studies using Gromacs. I have use Amber sb ildn forcefield and make topology file for ligand using Acpype. It shows error that the solv.gro file and topol.top file...
31 May 2021 6,776 2 View
I have added 1.AMBER14SB_parmbsc1 2: AMBER99 force field BSC1 in my working directory but it still gives the error- Residue 1 named DG of a molecule in the input file was mapped to an entry in...
02 March 2021 2,285 1 View
I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.
19 February 2021 5,207 2 View
I have a DNA sequence which has predictability to form G quadruplex . I need a software to generate a pdb of it which will form G quadruplex. I am using open Babel but I am not able to set the...
30 January 2021 6,468 4 View
I have used Autodock 4.2 for docking studies and trying haddock for DNA-Ligand docking. It shows an error and not supported DNA PDB file. Suggest a template for DNA and ligand PDB file and also...
30 December 2020 1,600 8 View
