AMBER Archive (2004)

Subject: AMBER: why delete water molecule

From: Helios Chen (p9890101_at_mail.ncku.edu.tw)
Date: Mon May 03 2004 - 23:18:49 CDT

Dear all, I saw some papers about run molecular dynamic with adding solvent(ex. TIP3P, TIP4P), but I have a question. Why they delete all water molecules in origin PDB file before adding solvent? Are there any difference between them? In another word, does the energy for adding solvent with deleting all water molecules differ from adding solvent without deleting any water molecules?

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