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?
Thank you
Pierre THEVENET
Le 06/04/2012 17:19, Justin A. Lemkul a écrit :
[email protected] 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
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