[gmx-users] SS bond forcing

[Justin A. Lemkul]

pithevenet at free.fr wrote:
> 
> Here is what I have done:
> 
> First, I created the .gro file with the command line: 
> 
> pdb2gmx  -f test.pdb  -o test.gro  -p test.top -ignh -missing
> 
> 
> Then, I added at the end of my test.top file the following lines (I double checked the atom numbers):
> 
> [ distance_restraints ]
> ; ai aj type index type' low up1 up2 fac
>   37 140 1   0     1     0.19 0.21 0.22 1
> 
> then, I done: 
> 
> editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic
> 
> grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp
> 
> mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0
> 
> 
> and finally get my new pdb file with:
> 
> editconf -f test-min.gro -o test-min.pdb
> 
> But it didn't seemed it had make the two sufur atom closer than if I didn't add the distance_restrain in the top file.
> 
> Did I do something wrong?
> 

Simple energy minimization is unlikely to give rise to the structural changes 
you need to bring these atoms close together.  Running a short MD simulation may 
work, though if the atoms are very far apart and you force them together 
quickly, you may have stability issues.

-Justin

-- 
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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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