Can anyone tell me how i can reterive complete bacterial data from KEGG?

I Want to download complete KEGG bacterial data please guide me how i can do that? or if any one have this data kindly send me. its not freely available for academic user too.

06 July 2019 8,918 6 View

Does PME requires periodic boundry condition using extend or restart file in namd?

Hi, I have a protein complex system, Initially i have minimized and equilibrate my system for 0.5ns. Then i want to slowly relax the side chain and back bone of my protein. i used all the restart...

09 October 2016 7,416 3 View

What is meant by Umbrella sampling and why it is require for PMF calculation in MD Simulation?

Hello, I want to know about umbrella sampling, and why it is required for potential of mean force for MD simulation?

08 September 2016 3,121 2 View

Which tools can plot inter-hydrogen bond interactions graph?

i want to plot total number of inter-molecular H_bond interactions between the drug compounds and target protein like below mentioned...

07 August 2015 4,118 13 View

Why Gromacs 4.5.6 does not generate .xtc file?

06 July 2015 6,637 9 View

How to convert amber topology and cordinates files into gromacs topology and cordiante file?

Hello, I want to run protein ligand MD simulation using Amber99sb force field. i generated protein topology files using gromacs easily but when i generated ligand topology using AmberTools15 and...

05 June 2015 4,816 3 View

How do I calculate binding free energy of simulated antigen-antibody structure?

I want to calculate binding free energy of antigen-antibody complex after 30ns MD simulation. I used MMPBSA but it takes approx 12 days for 1 ns (500 frames) of antigen-antibody complex in which i...

01 February 2015 3,036 15 View

Which is the best computational software to remodel antigen-antibody?

I downloaded PDB ID 4I3S it contains 16 missing residues in heavy chain of antibody as well as in antigen. I want to remodelled it before running the simulation. Which is the best computational...

10 November 2014 5,217 10 View

How can I calculate the half life of an inter-hydrogen bond?

06 July 2014 1,104 0 View

How can I calculate inter-hydrogen bonding between an antibody and antigen using pymol?

i want to calculate inter-hydrogen bonding between antigen and antibody using pymol. how i can calculate it and how i can get the hydrogen bonding log file?is there any way to get pymol log file...

05 June 2014 6,962 3 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

Why the results when using wall thickness and when using shell conduction are different in ansys fluent?

Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...

01 March 2021 9,537 2 View

Joint behaviour in Abaqus is not captured well?

I am working on roof joint and trying to simulate the behaviour in Abaqus. I am successful in running the model but the final graph does not follow the experimental curve in the negative direction...

01 March 2021 6,661 3 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View