11 November 2016 4 5K Report

Hello,

I am trying to run molecular dynamics simulation of a protein in water in GROMACS. The protein contains 21 subunits(chains). There are three types of subunits. I have attached a GFP to each of eight subunits(of one type) in chimera.

I am new to gromacs,and I am wondering how to choose appropriate forcefield and water model for the simulation of the protein?

I randomly choose OPLSAA force field SPC/E water model but error like this appeared,

"Atom HB3 in residue MET 1 was not found in rtp entry MET with 19 atoms

while sorting atoms."

Then I enter -ignh in my pdb2gmx command but there was error again with this message,

"Residue 27 named LYS of a molecule in the input file was mapped

to an entry in the topology database, but the atom CG used in

that entry is not found in the input file. Perhaps your atom

and/or residue naming needs to be fixed."

It would be very helpful if anyone could share some ideas.

Many thanks.

Dammar

Similar questions and discussions