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Joined: Mar 2006
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i have simulated a bio-molecular in a box of water. and i want to calculated the number of the hydrogen bonds between the bio-molecular and water molecules. i have read energy.doc and hbond.doc, but still have no idea. I wonder if you can tell me how to do that? thank you for your kind help.

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i am looking at coorman.doc to study coor hbond command. thank you.

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The Script Archive forum is a useful source of examples of how to do a number of things in CHARMM, including hydrogen bond analysis.
Read the coor hbond section of corman.doc VERY carefully, especially the part about having donors and acceptors defined for your water molecules.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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