[gmx-users] Chain merging problem (pdb2gmx)

[Ashutosh Jogalekar]

Hello
I have three peptide strands with the sequence HHQALVFFA. I am trying  
to create a .gro file of these. But I don' want to merge these chains  
together, as the N termini are not capped (NH3+)
When I do pdb2gmx, even when I am not using the -merge option, the  
program is still merging the chains together. Since they are actually  
separate in reality, this is causing many problems, not the least of  
which is that the charge on the system is being cited as +1, when it  
should be +3.
What should I do to get rid of this problem?
Thanks
Ashutosh Jogalekar
Emory University