[gmx-users] merge option in pdb2gmx

[Valentin Gogonea]

GMX users,

I am trying to make a bridge between two peptide chains using the 
specbond.dat file. It works only if the "merge" option in the pdb2gmx 
is used, but in this case pdb2gmx creates a bond between the two 
peptide chains which eliminates two of the chain termini (one from each 
peptide). Is there a way to avoid this elimination of termini?

Thank you for your help.

Valentin