Dear All,
I planned to use the method introduced in the Umbrella Sampling on-line
tutorial of Justin Lemkul
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html).
But if a peptide is surrounded by a protein, which means the opening of the
protein-complex is not large enough to allow the peptide to leave the protein
without significantly breaking the conformation of the protein in the
protein-peptide complex, is the Umbrella Sampling method still valid for the
binding energy calculation?
Will you please also show me in which part of the tutorial the direction of
pull-apart is defined? We should process it in a direction the peptide can
leave the protein, not the direction protein will bind the peptide much
strongly.
I am looking
forward to getting a reply from you.
Cheers,
Acoot
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
