You do not need to fix the copper in the calculation. There are must be some negative charged residues around the copper. Therefore, the copper will located at the place where it should be.
regards. -- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden At 2012-01-04 01:15:34,ljin1988 <ljin1...@126.com> wrote: Hello, I am a beginner of Gromacs, and I am working with enzyme that contains two Cu2+ ions in the active site. I have found two solution to treat copper ions and surrounding His residues. First solution is adding position restrain to these ions, while the second one is defining bonds between copper ions and surrounding His residues. I just wonder about which one should I adopt? Thanks very much.
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