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Questions related from Pallavi Agrawal
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 4,898 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 7,613 7 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 6,716 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 2,217 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 5,052 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 6,341 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 1,458 8 View
