[gmx-users] SS bond forcing
pithevenet at free.fr
Mon Apr 9 19:08:49 CEST 2012
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?
Le 06/04/2012 17:19, Justin A. Lemkul a écrit :
> pithevenet at 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 :
>> 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.
>> 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:
> Refer to the manual section and figures cited on that page for more
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