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
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