Pierre THEVENET wrote:
Thank you for your help, I tried to do as indicated in the link to send
to me, but it seems that it didn't change anything. Could you show me an
example, to better understand what I am doing wrong?
It would be better for you to show us what you tried, along with whatever
evidence suggests the restraints didn't work. There are several examples
provided in the manual, so the only things I would post as examples are already
available.
-Justin
Thank you
Pierre THEVENET
Le 06/04/2012 17:19, Justin A. Lemkul a écrit :
pitheve...@free.fr wrote:
Dear gmx users,
I try to use gmx to make some minimization. Unfortunatly, I have some SS
bonds which are not formed in my PDB because the S-S atoms are too
far away
to connect to each other. I saw at that page :
http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds
that it
is possible to force GROMACS to make bonds with sulfur atoms by adding a
distant constrains between the atoms.
Note that constraints and restraints are different.
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
But I didn't understand in which file it should be inserted and at which
step. Can you help me?
If you want to restrain S-S distances to force a more amenable
geometry for disulfide formation, what you need are distance
restraints in the .top:
http://www.gromacs.org/Documentation/How-tos/Distance_Restraints
Refer to the manual section and figures cited on that page for more
information.
-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
========================================
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