[gmx-users] Creating distance restraints between two atoms of different molecules

[Mustafa Tekpinar]

Hello everybody,
I am trying to put a distance restraint between two atoms of different
molecules, such as DNA and RNA . I created an index file that contains only
these two atoms. Then, I called gmx genrestr with this index file. Now, I
have an itp file, which includes a distance restraint.
However, I have two questions here:

   1. In positional restraints, the atoms numbers refers to the numbers in
   moleculetype section, not to the general gro file ordering. However, in
   my itp file, the numbers refers to the gro file numbering for both of the
   atoms. Is this correct?
   2. Where should I call this itp file in my topology file?


Thanks in advance for your help,
Mustafa


-- 
Mustafa Tekpinar, PhD

Pasteur Institute
25-28 Rue du Dr Roux
75015 Paris, France