[gmx-users] SS bond forcing

pithevenet at free.fr pithevenet at free.fr
Tue Apr 10 09:24:34 CEST 2012

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?

Thank You.


Pierre THEVENET wrote:
> 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?

It would be better for you to show us what you tried, along with whatever 
evidence suggests the restraints didn't work.  There are several examples 
provided in the manual, so the only things I would post as examples are already 


> Thank you
> 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 :
>>> 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


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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