Thanks a lot for the help, that will do well enough, but require me to redo
some things I did before. As far as you know there is no way to have multiple
constraints using the center masses of the peptides? Thanks.
_________One thing which you could do is to write your three proteins into
one molecule definition (if you use .itp files, then make one .itp for
all three). Then at the end of the molecule definition you can add
the constraints.
To merge the three proteins is rather easy but cumbersome, you must shift all
the atom numbers of the second and third protein. So if each protein would have
100 atoms, protein2 would start with atom 101. depending how big your proteins
are it could be better to write a script which merges the three proteins
instead of doing it by hand.
Greetings
Thomas
___________________Or just re-create the topology with pdb2gmx -merge.
-Justin
___________________
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