[gmx-users] Re: One molculetype for 3 proteins

Francesca francesca.stanzione at unina.it
Thu May 24 22:28:04 CEST 2012

I had the same problem and I didn't  find any way to do it. So i created new
residues for the terminals, and I added them to the forcefields files.
Example: if my first COOH terminal was a SER i created a SERT residues and I
used the COOH values taken from ASP , and the same procedure was used for
the next Nterminal...in that way I have a SERT in the list of amminoacids
and when you process the pdb2gmx you have 1moleculetype, but you have 3
different chains each with its terminals.  Be careful to use correct values
and add these residues to the list of amminoacids in the forcefield
directory. I used that method and I could apply the distance restraints.


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