Kalindu Fernando

6 Questions 13 Answers 0 Followers

Questions related from Kalindu Fernando

How do I calculate the persistent length of a peptide using MD simulation ?

Hi all, May I know how to calculate the persistent length of a peptide using MD simulation trajectory ? Thank you in advance !

29 June 2023 5,465 1 View

How can I modify MD forcefield files for a peptide contain unnatural amino acids?

Dear All, I have a peptide having the following synthetic amino acid, that needs to simulate using Gromacs. I have selected CHARMM36 force field and the initial topology for the synthetic amino...

19 July 2022 2,844 0 View

How can I make the .hdb(hydrogen data base) entry for new molecule ?

Dear all, Can anyone support me to get the accurate .hbd entry for the "HA'' hydrogen in the attached molecule? My following entry gives an error in Gromacs I also want to know the "-C" meaning in...

26 January 2022 3,182 2 View

What are the possible approaches for MD simulation of long RNAs ?

I want to do an MD simulation of GFP (Green Fluorescence Protein ) mRNA. But it's too long containing around 800 bps, impossible to do all atomistic simulations. May I know what are the possible...

17 January 2022 6,167 4 View

Why doesn't Topolbuild generate dihedral angle parameters at recommended setting for OPLSAA?

Dear all, I am simulating a peptide with a few unnatural amino acids in Gromacs. I used Topolbuild to get topology files for the peptide. I cannot get dihedral angle parameters when I use...

31 December 2021 8,788 4 View

How can I run a peptide with an artificial amino acid and a linker on GROMACS?

I am trying to do an MD simulation of a peptide containing artificial amino acid (modified cysteine) and a linker as follows in Gromacs. I do not have forcefield parameters for these new molecule...

15 December 2021 8,359 5 View