Dear Helios:
Although it has been advised that the crystal waters should be removed,
one certainly has the option not to do so. It is probably a good idea to
retain the crystal waters. However, a technical challenge for not
removing the crystal water is the assignment of hydrogens. You probably
can try to assign these hydrogens at randomized orientation and optimize
them by MD. But you have to write your own code to do it.
yong
On Tue, 4 May 2004, Helios Chen wrote:
> 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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Received on Tue May 04 2004 - 15:53:00 PDT
