Dimuthu Kodituwakku

7 Questions 6 Answers 0 Followers

Questions related from Dimuthu Kodituwakku

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...

25 August 2020 8,451 1 View

How to simulate a protein with FAD using amber?

My protein (GoX) contains a FAD coenzyme which is important for protein's function. How do I simulate this protein using amber as it does not provide force fields for co-enzymes?

02 March 2020 4,806 3 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.

27 January 2020 8,447 1 View

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

I have performed an MD simulation for 10 ns. After going through output pdb files I found that my 2 double bonds have been converted to single bonds? Is that possible?

17 October 2017 6,040 2 View

How to view ligand-protein non bonded interactions from discovery studio?

I have an output file of a molecular dynamics simulation for a protein-ligand complex. But I can't view the ligand through DS visualizer. It says my ligand is undefined.

09 October 2017 3,008 9 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...

07 October 2017 1,246 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...

25 September 2017 1,490 3 View