7 Questions 15 Answers 0 Followers
Questions related from Kalindu Fernando
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 5,520 1 View
Dear All, I want to generate topology files for the following peptide having an aliphatic linker in the middle and an unnatural amino acid to perform MD simulation using GROMACS. I tried to...
29 August 2022 3,152 0 View
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 2,930 0 View
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 3,240 2 View
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 6,230 4 View
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 8,849 4 View
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 8,422 5 View
