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 <[EMAIL PROTECTED]> 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
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