jalemkul at vt.edu
Thu Apr 5 00:48:55 CEST 2018
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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