James Starlight wrote:
Francesca,
Yes I suppose this is good aproach for the generation of position
restricktions on the desired atoms. But I want to restrain the distance
between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of
two different residues).
How many restraints do you need to create? If they are this simple, you can
write them yourself using a text editor in conjunction with manual section
4.3.4. Using genrestr is only really helpful when you require a network of
distance restraints between the atoms of a given group. If there are only a few
to create, it's actually more work to use make_ndx and genrestr than it is to
fire up your favorite text editor.
Also I want to restrain some dihedral angles in the desired rotameric forms.
See manual section 4.3.3 and
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints.
In literature I've found that peple have dome the same things in Gromacs
but I could not find detailed algorithm of such methodology :(
All relevant equations are provided in the manual, and examples are provided
either there or on the Gromacs site. If you need further information, ask a
specific question related to what you can't find or don't understand.
-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
