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Questions related from Sadaf Rani
Dear Gromacs users I am doing a test calculation in MD simulation between ligand and a protein residue for bond angle and dihedral restraints. I have set them in my topology file as below:- ;...
02 February 2020 852 3 View
Dear Gromacs users I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand when I run pdb2gmx it gives me error:- Fatal error: In the chosen force field there is no residue type...
02 February 2020 4,740 3 View
Dear researchers I am facing this error during the free energy calculation of protein-ligand for which I have applied restrained to some atoms of protein residue and ligand. A list of missing...
01 January 2020 5,267 4 View
Hi Gromacs users I am trying to set a protein-ligand system in gromacs for MD simulation. I took topology and gro file from an external source. Now I combine the gro file of ligand and protein...
11 November 2019 6,217 8 View
Dear researchers Need your expert suggestions please. I am trying to get protonation states of my protein ligand by using pdb2pqr webserver version 2.1.1. However; when I get result propka file...
08 August 2019 4,966 12 View
I want to run MD simulation of my protein that is 479 a.a long. I found 6 bad contacts in my protein by the process mentioned in tutorial....
05 May 2019 7,835 10 View
I am following amber tutorial with HIV protease Can any one suggest me from where I can find this particular file?mentioned in this command Copy parameters of ions to your working directory...
04 April 2019 4,028 4 View
I am trying ligand protein gromacs tutorial for my protein ligand MD when I come to the command python cgenff_charmm2gmx.py JZ4 jz4_fix.mol2 jz4.str charmm36-nov2018.ff it says that This script...
04 April 2019 4,729 1 View
I started protein ligand MD simulation in gromacs for 10ns. However due to cluster shutdown I had to restart it again. Md.tpr file of md is formed but it do not include portion after restart; How...
02 February 2019 9,782 3 View
I am running a protein ligand MD simulation using gromacs. I have started npt equilibration for 500000 nsteps (1ns). After a computer shutdown at 170500, I started restart using following...
10 October 2018 1,187 1 View
I am running a protein ligand complex MD simulation for 10ns. My question is how much nvt and npt simulation time is required before running production run?I am new to MD and gromacs, Any...
10 October 2018 1,200 0 View
I am running a protein ligand MD simulation in gromacs, when I generate ligand.gro file using this command gmx_mpi editconf -f bg6_ini.pdb -o BG6.gro it gives following at the end Read 76...
09 September 2018 8,274 4 View
I am working on protein ligand MD in gromacs, Half of my protein is outside the box in solv.gro. How can I make them inside box?
09 September 2018 4,536 0 View
I am running a protein ligand MD simulation using two ligands in gromacs, but when I prepared solv.gro and newbox.gro my protein is not central inside the water box. I used following commands:...
09 September 2018 6,635 3 View
