Can double bonds get converted to single bonds during an MD simulation?

More Dimuthu Kodituwakku's questions See All

How to build a topology for a novel molecule in CHARMM?

Hi, I'm trying to attach a carbonyl linker to Lys so that I can attach a PEG molecule to it. I have attempted so far by combining Lys , N-terminal and C-terminal topology data . But I'm having...

24 August 2020 8,395 1 View

How to combine a ligand and protein topology file in NAMD?

I'm fairly new to NAMD. I have generated a topology file for my ligand through CGENFF but I do not know how to combine topology files of ligand and the protein.

26 January 2020 8,411 1 View

Which method of RMSD calculations is the best for protien analysis?

I have performed an MD simulation for a protein-ligand complex for 10ns. Now I need to analyze the effect of ligand binding and MD simulation on the protein structure. Which RMSD method is the...

06 October 2017 1,212 3 View

How to calculate energy of a protein-ligand complex?

I have done an MD run for a protein-ligand complex using gromacs in a box containing water. I want to calculate free energy of the protein-ligand complex alone without water. Any suggestions.Thank...

24 September 2017 1,449 3 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How the parameters (such as Mw, Chemical bonds, polymer bland and so on) affect the mechanic property of polymer (such as storage, loss modulus) ?

Anyone can recommend any books on such topics? Thanks in advance.

02 March 2021 8,457 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

Martin Klvana

Bonds, in classical mechanics, are "springs that stretch and contract" ---- and this behavior can be tuned by setting the equilibrium spring length and rigidity.

Your observation means that there is something wrong with your force field model: equilibrium bond length, force constant, partial atomic charges, . . .

Dimuthu Kodituwakku

Thank you for all your answers. Robin M.Betz how to convert my pdb file to .psf or .prmtop format?