[gmx-users] Making Disulfide Bonds

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 28 16:30:21 CEST 2012

On 4/28/12 10:25 AM, James Starlight wrote:
> Francesco,
> Thanks, I find your aproach very handfull :)
> Justin,
> in that example I've defined in minim.mdp

This would have been useful to state up front.  Your previous question implied 
that you didn't know if any special keywords were necessary in the .mdp file, 
hence why I pointed it out.  Complete information is always more effective.

> *disre = simple
> ***disre_f = 5000

The latter is not a real keyword, but I'll assume you've done it right in the 
.mdp file.

> in the topology.top I've included
> ** [ distance_restraints ]
>     ; ai aj type index type’ low up1 up2 fac
>        1 10  1    0     1    0.18 0.20 0.22 1.0
> where 1 and 10 the numbers of the S atoms of both Cys residues. and 0.2 is the
> disered distance between wich I want to obtain after such minimisation.
> **
> As the consequence no changes have been detected after such CG minimisation :(
> What I've forgotten ?

It doesn't seem like you've forgotten anything.  Depending on how far away the 
atoms are from one another in the starting structure, perhaps EM is simply not 
creating large enough structural changes to impose the desired geometry.  A 
distance restraint is simply a biasing potential, it is not a guarantee that 
certain geometry will be imposed, just made more likely.  Perhaps other aspects 
of the structure are preventing it from changing much.  Perhaps you need more EM 
steps, or maybe run a few steps of in vacuo MD to see if the structure adjusts.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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