Dear Justin:

What I mean is can I calculate the free energy of restraining the ligand in the 
binding site, since I put on distance restraint to the ligand and the protein?

Regards
Chunxia

Chunxia Gao wrote:
> Dear Justin,
>
> If I apply the pull code to the distance restraints, can I calculate the free 
> energy of those restraints through g_bar? In what way?
>

The pull code and free energy code are independent.  I see no reason why you
could not proceed in the same manner as the free energy tutorial describes, but
with the addition of your restraint.

> and the pull code can only be applied to distance restraints, right? not 
> angle or dihedral restraints?
>

Correct.

-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

Reply via email to