14 Questions 28 Answers 0 Followers
Questions related from Sadaf Rani
Dear Researchers, I need your help in understanding the results of a semi-empirical calculation. For a reaction barrier if the transition state is coming at about 100KJ/mol. Does it mean that...
26 September 2022 6,008 0 View
Dear all I am simulating a protein-ligand complex. During the course of simulation, the cofactor moves far away from the substrate. I want to add distance restraints between protein backbone and...
15 August 2021 8,864 1 View
Dear All Can anyone please help me to understand the SASA plot calculated in vmd? as attached below:-
07 January 2021 4,462 0 View
Dear Gromacs users I am facing a problem between different versions of gromacs for gmx pdb2gmx. I have a protein-ligand system, I did all the necessary steps mentioned in gromacs manual for...
28 April 2020 1,797 3 View
Dear Researcher I am having trouble during free energy calculation in gromacs as below:- I ran an MD simulation for 3ns and from the last coordinates started a free energy calculation for 3ns. My...
25 March 2020 5,548 9 View
Dear Researchers I have two proteins crystal structures from RCSBD, one is a monomer with two ligands and the other is a dimer with one ligand in each monomer. Both have the same sequence of...
26 February 2020 350 5 View
Dear researchers I want to calculate the binding free energy of ligand in the protein-ligand complex. I have two ligands in the complex could you please guide me how can I apply restraints on...
10 December 2019 10,060 4 View
Dear Gromacs users I want to do MD simulation for my protein but when I run pdb2gmx command I am facing this error:- WARNING: WARNING: Residue 197 named PRO of a molecule in the input file was...
13 November 2019 5,652 3 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...
10 November 2019 2,971 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...
04 August 2019 6,663 9 View
Hello every one I have two protein structures having different ligands but sequence are similar almost. I aligned the two so that both ligands come together now I want to save the aligned...
22 June 2019 8,352 4 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....
15 May 2019 1,900 8 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:...
11 September 2018 9,364 3 View
I am new to amber any trying to use xleap to make a tetrapeptide tuftsin. After solvation with TIP3PBox 14.0 iso, when I try to save the inpcrd and prmtop file using command saveamberparm foo...
01 January 1970 7,906 2 View
