Dear Amber users,
The Polymer I built in xleap has some residues intercalating each other i.e bonds going through inside of aromatic ring of residues. I tried variety of minimizations starting from restraining heavy atoms to restraining whole residues to not restraining any atoms. I could get rid of one or two of these intercalations but there are few more which are intact. I also tried moving around the atoms and then minimizing but it didn’t help. I went ahead with MD simulation and checked the output trajectory file. I could still see those intercalations. I have attached a snapshot of my issue. Any help is greatly appreciated.
Thanks,
Ashar
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Received on Fri Apr 10 2015 - 17:00:03 PDT
