madhumita das wrote:
Hi GROMACS users,
I have generated topology and gromacs files using acpype.py .This is a
membrane protein and thus to be simulated along with membrane. How can I
use AMBER forcefield instead of GROMOS force field. Should I do the
same as stated in the GROMACS tutorial in which GROMOS force field has
been used?
You should not combine different force fields, so no, you should not simply
follow that tutorial and attempt to use a ligand topology designed for an AMBER
force field. The general workflow is largely the same, however, so you can
apply the logic of the tutorial to whatever your system is.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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
