[gmx-users] charmm-gui

[Justin Lemkul]

On 4/4/18 4:49 PM, m g wrote:
> Dear Justin, I am using charmm-gui to generate the lipid bilayer according to CHARMM36 force field. I embed the peptide in bilayer. Is the file produced for peptides, which is based on the CHARMM36, can be used in simulation with GROMACS(because I want to used 4 peptide in my bilayer)? Can I extract peptide from bilayer and I set four of that in the bilayer again? Can I used the CHARMM27  for peptide, and CHARMM36 for bilayer? is it true? Would you please help me?

I don't really understand the question. If you're building different 
systems, you can just have CHARMM-GUI build everything rather than 
trying to hack the files.

I also don't recommend using CHARMM22/CMAP for the protein (please note: 
there is no such thing as CHARMM27 for proteins, it's a common 
confusion). The latest CHARMM36 parameters are superior in all regards, 
particularly with the latest CHARMM36m modification for proteins.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================