On Tue, 15 Jan 2008 08:20:05 -0600
eddie mendel <[EMAIL PROTECTED]> wrote:
Greetings Gromax users!
I am trying to do free energy calculations using a Go-model Hamiltonian
simulation, and I was wondering if GROMACS has such capabilities.
I was planning to use CHARMM but I found a problem at a server that builds
the respective Go-model Hamiltonian from a pdb file
I do not know anybody who as used a Go-model in GMX but it should not be
so difficult using tabulated potentials!
this is the website in case you are interested:
http://mmtsb.scripps.edu/webservices/gomodel.html
What is wrong with the website server? Does it give a wrong "topology"?
We have been using it for a peptide and that would be nice if you could
detail the "bug".
Please let me know any suggestions you may have. My protein has around 500
residues and hence I think a Go-model is the only viable
option I have.
Depends on what you are after. We have developed a Coarse Grain model
for proteins and it can handle enormous systems without problems. It
should be out in a few months.
XAvier
Thanks for the advice beforehand
Eduardo Mendez
PhD Candidate and so forth
Department of Biochemistry
University of Saskatchewan,
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
