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• Gromacs And Modified Residue
  Hi, i'm trying to run an MD simulation of a protein with a tRNA and i'm getting an error that it ...
• Gromacs-Molecular simulation of a protein and ligand
  In gromacs after setting the forcefield, I get an error saying that my residue is not found in th...
• Changing the conformation of bound protein chain to its unbound state
  If I want to carry out an unbound docking of the 2 chains of a hetero-dimeric protein but the ind...
• BioPython: Residues size differ from position
  I'm currently working with a data set of PDBs and I'm interested in the sizes of the residues (nu...
• Trouble Interpreting Warning Messages When Performing Homology Modeling With Gromacs And Procheck
  Hi experts, Need advice! I performed homology modeling using HHpred with two approaches: 1) Loc...
• What is the basis of inputting the emtol parameter in the minim.mdp?
  My protein has 596 residues that I'm trying to simulate in GROMACS 5.1. Can anyone explain the b...
• RNA-Ligand simulations with GROMACS
  I want to perform some molecular dynamics simulations with GROMACs using a RNA-Ligand complex i h...
• Biopython to compute the distance between residues
  Hello, I am trying to use Biopython to find the distance between the alpha carbons for a pair of...
• stereochemical issue after MD simulation
  Hi everyone, I need suggestion from you all. I have performed MD simulation of predicted protein...
• Disrupted protein structure after 5 nanoseconds of GROMACS molecular dynamics
  Hello, I have been trying perform a molecular dynamics using GROMACS. The idea is to simulate a s...
• error 'LIG ' not found in residue topology database in gromacs how to solve
  Hello All I am trying to minimize a ligand only without any protein which is cholesterol but it ...
• "Atomtype O not found" error in gromacs 5.1.1
  Hello, I am doing MD simulation for Protein-ligand docked complex using Gromacs 5.1.1. When I t...
• Energy minimization error using gromacs
  Hi all, I'm new in molecular dynamics simulation. During energy minimization of my protein in gr...
• Error: Parsing Pdb File With Biopython
  I am trying to parse a PDB file and also trying to extract some Model, Chain, Residue and Atom o...
• Problem using a custom blast database in tblastx
  Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA ...
• grompp error : atom name in topol.top and solv.gro does not match
  hello,  I am using gromacs to energy minimize Protein -Ligand complex. I have performed all the ...
• An error message while installing gromacs on windows 10 (Linux bash shell, ubuntu)
  Hello, I would like to install gromacs on windows 10 (Linux bash shell). I followed the instruct...
• PDB file modification for homology modeling
  Hello, I have a bit of a complicated query here and I'd much appreciate some help if possible. I...
• How To Identify Rotamer States From A Pdb ?
  Do you know of any simple code or package that simply outputs the rotameric state of a given resi...