tsjerkw at gmail.com
Fri Sep 24 21:15:58 CEST 2010
Using C N CA CD instead of C CA N C inverts the improper dihedral. And
unlike all atom force fields, you can start from an L-proline :)
On Sep 24, 2010 10:46 AM, "Stefano Pieraccini" <Stefano.Pieraccini at unimi.it>
Dear Gromacs users,
I would like to use gromacs to simulate a peptide containing a D-proline
using the opls force field. I guess that, considering that L- and D- PRO
differs only for chirality, the two a.a. topologies should little differ,
and that an improper torsion and/or torsional terms should be modified in
D-PRO topology with respect to L-PRO, but I am not sure on how to modify the
improper torsion ( it is _C CA N CD in L-pro) and if it is correct to do so
or only torsional terms should be modified.
Thank you in advance
gmx-users mailing list gmx-users at gromacs.org
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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users