[email protected] 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
--
========================================
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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