Meiling Li

4 Questions 1 Answers 0 Followers

Questions related from Meiling Li

How to optimize a protein, molecule and POPC system?

Hello, I want to use AMBER to run a simulation of a membrane protein, small molecule and POPC bilayer membrane complex system, and the complex parameter files .inpcrd and .prmtop have been...

24 September 2023 3,942 1 View

How to turn the gromacs' top and gro files into amber's parm and rst files?

Hello, I want to use the final structure of gromacs after 100ns to run a GaMD simulation with amber software. So，I should turn the gromacs' top and gro files into amber's parm and rst files? I...

29 August 2023 2,022 1 View

Gmx_MMPBSA error about MPI?

pHello! I have run a 100ns trajectory of membrane protein and small molecule using gromacs software with CHARMM36 force field, and then I wanted to calculate ligand binding energy using...

21 July 2023 3,119 2 View

Nonnatural amino acid NAL parameter CHARMM36 ?

Hi! I have a peptide which has nonstandard amino acid NAL at the N-terminal and C-terminal, and I want to use CHARMM36 force field to generate it’s parameters, there are no dihedral parameters...

03 February 2023 3,261 0 View