[gmx-users] cyclic peptide: adding constraints

[Tsjerk Wassenaar]

Hi,

Just as a note. You don't want to use distance restraints for making a
cyclic peptide. This will not give you correct behaviour of the
backbone. You want to have a bond, some angles, dihedrals and proper
exclusions. You want a cyclic peptide. The best thing is to reread my
previous email regarding the linkage of your terminal residues and do
the homework I gave there ;)

Best,

Tsjerk

On 10/31/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Giacomo Bastianelli wrote:
> > I tried to include the distance contraints in my .top file as follows:
>
> Distance "restraints" are what you want, not "constraints". Read 4.3.4
> in the manual.
>
> Notwithstanding, the stuff below should work so long as your constrained
> atoms are in the same molecule, you've put the [ constraints ] directive
> in the right position with respect to the [ molecule ] directive, the
> molecule is correctly defined, and the starting geometry is not too far
> from the constrained distance.
>
> > [ 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)
>
> grompp thinks the molecule to which you are applying constraints has
> only 1 atom (hence 1-1). Probably you've #included some ion just before
> this, and thus have your [ constraints ] directive associated with the
> wrong [ molecule ] directive, or made some catastrophic error with your
> topology.
>
> > I thought that the function number 2 would have not create
> > the bond between the two atoms but just constrained the distance.
>
> Yes.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336