Kalindu Fernando

4 Questions 9 Answers 0 Followers

Questions related from Kalindu Fernando

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 2,788 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 3,174 2 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 8,779 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 8,351 5 View