24 Questions 13 Answers 0 Followers
Questions related from Bijaya Pathak
Dear all, I'm trying to carry out metadynamics for a cyclic dimer system using Cp2k . I want to use center of mass to center of mass distance as my collective variable. Can anyone suggest me how...
02 February 2024 6,483 0 View
I'm trying to dock protein with DNA. The only problem is that there is no experimental data available for my system. Based on the limited data, I did dock the system using HADDOCK. Now my...
13 September 2023 3,725 2 View
Hello all. I need to calculate the average structure of a protein from a 100ns trajectory. I came across two commands - gmx cluster and gmx covar. I tried gmx clusters, but the structure I got...
07 August 2023 8,643 1 View
I need to generate force field for an organic molecule with a strained structure. The ring has C=O group attached to it with an angle 90 degree. I tried OPLS, GAFF and CGenFF , but in all the...
08 June 2023 8,851 1 View
Hello all. I'm trying to calculate the binding energy for some specific residues and a metal in my system using MMPBSA. The problem I'm facing is , everytime I specify residue index, its showing...
27 May 2023 8,104 0 View
I'm trying to optimize a large number of structures( above thousand) with 60 atoms in each. I need a cheap method for optimization. I came across DFTB , which can be helpful for my calculation....
02 April 2023 199 3 View
Hello all, I am using CP2K software for free energy calculation from metadynamics. My problem is it generates a lot of files without giving much information regarding them. Can anyone help me out...
16 March 2023 2,266 0 View
I'm trying to carry out metadynamics for a system, where my collective variable is bond length. Is there way to decide how to set values for height and width ? I tried with two different values...
30 January 2023 6,414 3 View
Dear all, I am working with a protein for which structure is not known. From the peptide sequence, I modeled the structure which has three zinc finger domain. My next task is to insert zinc ions...
18 November 2022 8,492 0 View
Hello all. I have a .gro file, from which I have to delete certain number of hydrogen atoms from specific residues. I tried doing it manually, but the atom numbers get mixed up and the file does...
16 November 2022 4,203 2 View
Hii all. I have a sequence of protein with me , for which the structure is not known yet. I have to model the structure using the sequence . I have got to know that pymol can be useful for such...
07 March 2022 4,111 4 View
Hello all. I am working on a ligand-dmso system using GROMACS. My system is supposed to be neutral but it is showing that it has an overall charge of 0.022153. I believe this is happening due to...
13 February 2022 8,158 3 View
Hi all , I'm trying to obtain stacking energy profile for two solutes using umbrella sampling. For that I need to fix the distance between them initially. I start with the desired separation,...
21 December 2021 9,959 2 View
Dear all, I have been trying to perform an MD simulation using Gomacs. My system has two ligands in DMSO solvent. While performing the NPT equilibration , I'm getting the following : Fatal error...
20 December 2021 3,833 3 View
Hi all, I'm trying to calculate the free energy profile for my system using umbrella sampling method. I'm new to this method and need to correct the PMFs obtained for volume and entropy...
16 December 2021 9,950 3 View
Hi all. I was trying to plot 2D- number density map of a system . I generated the .xpm file using gmx densmap command. After getting the the .xpm file, I used gmx xpm2ps command to generate .eps...
25 October 2021 7,736 1 View
Hi. I'm learning molecular dynamics simulation, where I came across different types of forcefields like CHARMM, AMBER, GROMOS, OPLS . What are few differences between them ?
04 October 2021 5,436 4 View
Hi all. I was wondering if its possible to mix Gaff with Amber force field . If yes , how to do it ?
04 October 2021 7,741 3 View
Hi there. I'm a beginner of QM/MM and been trying to run ONIOM calculations. I ran the calculation and got output file as well . However, i don't know how to interpret the data. It looks almost...
09 July 2021 2,754 3 View
Hi all, I'm trying to model a protein using the amino acid sequence using the Software Modeller. I'm uisng Modeller-10: difficult modelling which models a sequence based on low identity to a...
01 January 1970 565 3 View
I have a PDB file . I have to remove hydrogen atom from CYS residues. I manually did it and when I'm running pdb2gmx command, it shows error about the hydrogen atoms. I tried -ignh flag but it...
01 January 1970 3,818 3 View
Hello everyone. I am having a problem with calculating angle using gmx angle. When I calculated the angles using the command I got certain values. However, using VMD I could see the angles are...
01 January 1970 8,891 1 View
Hello all. I need to calculate the average structure of a protein from a 100ns trajectory. I came across two commands - gmx cluster and gmx covar. I tried gmx clusters, but the structure I got at...
01 January 1970 6,821 4 View
Dear All, I have come across something strange while doing RMSD calculation. I calculated the RMSD of a mutated protein using the .tpr file generated from Wild type and it does the calculation...
01 January 1970 2,006 4 View
