20 Questions 116 Answers 0 Followers
Questions related from Anwesh Pandey
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...
10 October 2019 7,040 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...
07 July 2019 2,865 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!!
07 July 2019 8,753 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...
06 June 2019 5,124 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?
05 May 2019 5,815 1 View
Is there any software which could mine data from downloaded research articles (pdf format) as per one's requirement?
10 October 2018 4,016 5 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...
10 October 2018 2,642 3 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...
07 July 2018 448 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...
05 May 2018 5,502 2 View
Can someone let me know about what is and how to perform, Umbrella Sampling in Molecular Dynamics Simulations, performed via GROMACS?
05 May 2018 6,921 5 View
After having had done molecular dynamics simulation i need to set up QM/MM calculations, kindly suggest some tutorial for the same; which could illustrate the need as well as the methodology for...
03 March 2018 3,177 4 View
Please let me know about how to perform MMPBSA/MMGBSA Calculation after having had done Molecular Dynamics Simulation of Biological Systems?
03 March 2018 3,888 4 View
I am carrying out molecular dynamics simulation of drug-dna system; after having had removed the nucleic acid from the complex when i proceed to to the MD via AMBER force field in UBUNTU system i...
03 March 2018 1,083 2 View
I am getting following error while doing MD Simulation, how to remove it?? Fatal error: number of coordinates in coordinate file (solvated.pdb, 24482) does not match topology...
02 February 2018 8,967 2 View
how to analyze the output files obtained via molecular dynamics simulation using Gromacs by command line? kindly suggest?
02 February 2018 8,326 6 View
Hi, i have to perform MD simulation of a no of Drug-DNA complexes (for now, its just 14; but i have over 50+ docked complexes). Can anyone suggest fast and reliable methods for the same?
12 December 2017 3,680 4 View
i hv several ligands and a receptor, say, 7ligands and 1receptor. now i am preparing .gpf file for all the possible combinations manually using autodock software. but i found that all those .gpf...
10 October 2017 411 4 View
again when we perform MD simulation of Drug-DNA complexes; we do Equilibrium MD Simulation. Can we perform Non-Equilibrium MD Simulation also or not for such systems? Also if we can, the what are...
10 October 2017 2,446 2 View
whenever we perform MD simulation (although i have not yet started doing MD of my complexes); we provide water as the solvent or water environment; why can't we use any other polar/non-polar...
10 October 2017 9,196 1 View
Drug-DNA Interactions: Intercalating Drugs
04 April 2017 3,057 0 View
