Re: [gmx-users] Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose

Hi, Asking for "the number of hydrogen bonds" is ill formed. Between what and what? Mark On Wed, 25 Jan 2017 09:48 Adarsh V. K. wrote: > Dear all, > > Protein-ligand complex MD simulation using Gromacs 5.1.4 (Drug discovery) > > Can you please tell me command for

[gmx-users] Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose

Dear all, Protein-ligand complex MD simulation using Gromacs 5.1.4 (Drug discovery) Can you please tell me command for Number of Hydrogen bond plot? It is # gmx hbond... But what option we have to choose, apart from Ligand (13) Is it (option after the command), protein protein-H side chain

Re: [gmx-users] Protein-Ligand Complex MD simulation ; Command for Number of Hydrogen bond plo

On 1/13/17 10:51 PM, Adarsh V. K. wrote: Dear all, Protein-ligand complex MD simulation using Gromacs 5.1.4 Can you please tell me command for Number of Hydrogen bond plot? and Other interactions between protein and ligand? gmx hbond calculates hydrogen bonds. Select the protein and the

[gmx-users] Protein-Ligand Complex MD simulation ; Command for Number of Hydrogen bond plo

Dear all, Protein-ligand complex MD simulation using Gromacs 5.1.4 Can you please tell me command for Number of Hydrogen bond plot? and Other interactions between protein and ligand? Regards, Adarsh V. K. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

Hello, You may follow " http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/ " Everything will go fine Good luck Amir On Wed, Dec 21, 2016 at 8:50 PM, Adarsh V. K. wrote: > Dear all, > > We have a 419 amino acid long protein and planned

[gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

Dear all, We have a 419 amino acid long protein and planned Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. 1. What sought of MD simulation we have to perform?. 2. Restrain protein alone or Restrain both protein and ligand during simulation?. 3. What is the exact command

[gmx-users] Protein-Ligand Complex MD simulation

Dear all, We have a 419 amino acid long protein and planned Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. —Whether the protein and inhibitor complex stable —Did the inhibitor remain in the active site pocket or did it fall out during the simulation —What factors

[gmx-users] Protein-Ligand Complex MD simulation

We have a 419 amino acid long protein and planned for Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. —Whether the protein and inhibitor complex stable —Did the inhibitor remain in the active site pocket or did it fall out during the simulation —What

[gmx-users] Protein-Ligand Complex MD simulation

Dear all, We have a 419 amino acid long proteing and planned Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. —Whether the protein and inhibitor complex stable —Did the inhibitor remain in the active site pocket or did it fall out during the simulation —What factors contributed

Re: [gmx-users] protein ligand complex MD simulation

Hi Ashan, This (from the manual, section 4.3.5) https://dl.dropboxusercontent.com/u/50317782/distance_restraints_gromacs.png or this http://www.gromacs.org/Documentation/How-tos/Distance_Restraints will help. Best, Sajeewa On Thu, Dec 8, 2016 at 5:35 AM, ashan dayananda

[gmx-users] protein ligand complex MD simulation

Dear Researches, i'm currently doing a MD simulation of a protein and a ligand.i want to restrain the distance of two amino acids in the active site to 4.0 angstroms. can any one help me to perform this task. Thank you Regards Ashna -- Gromacs Users mailing list * Please search the archive at