[gmx-users] cyclic peptide: adding constraints

Giacomo Bastianelli gbastian at pasteur.fr
Mon Oct 30 17:53:47 CET 2006

I tried to include the distance contraints in my .top file as follows:

[ constraints ]
; atom1    atom2    function    distance
1    245    2    0.133

this is my output:

Fatal error:
[ file "1NB1.top", line 1665 ]:
             Atom index (245) in constraints out of bounds (1-1)

I thought that the function number 2 would have not create
the bond between the two atoms but just constrained the distance.



Mark Abraham wrote:
> Giacomo Bastianelli wrote:
>> Dear Gromac's users,
>> since I had several problems trying to setting up a cyclic version
>> of my protein (tried editing topology and modifing the specbond.dat 
>> file),
>> I was wondering if it could be possible to add a constraint between
>> the N-term and C-term of my protein in a way to simulate my peptide
>> bond.
> Yes, they're called "distance restraints" and there's a description in 
> the manual.
> Mark
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