[hisano]

Dear all,

Tutorial 6.2 suggests me to use the CHARMM-GUI web site to obtain a model of a membrane-embedded protein and associated parameter and input files for GENESIS. But how can I obtain them if I don’t want to upload my unpublished protein structure data (a protein-ligand complex) to the public web site?

Best regards,

Tamao Hisano

[oshima]

Hi Hisano-san,

I’m not so familiar with the modeling software or service for membrane proteins, so I cannot propose an alternative way. The CHARMM-GUI uses CHARMM (not force fieled but software) for setup of the system and save input files for CHARMM. Why don’t you build your system by modifying the CHARMM input files as a reference? The original paper of CHARMM-GUI (PLoS ONE, 2, e880 (2007)) may help you.

Thanks,

Hiraku Oshima

[hisano]

Dear Oshima-san,

Thank you for the suggestion and the reference paper. If I understand correctly, I can get GENESIS input and parameter files to run MD for my unpublished protein by modifying CHARMM-GUI files generated for a protein other than the unpublished one. I will try.

Best,

Tamao Hisano