[gmx-users] Re: Constraints between multiple molecules

Michael McGovern mpmcgovern at wisc.edu
Fri Aug 6 18:18:01 CEST 2010

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.

___________________Or just re-create the topology with pdb2gmx -merge.



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