AMBER Archive (2005)

Subject: AMBER: Solvate question?

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Mon Jun 06 2005 - 05:30:44 CDT

Hi user:
I try to solvate my protein with the acetonitrile model in
http://pharmacy.man.ac.uk/amber/. I download ch3cn_210.pdb, prep.ch3cn and
frcmod.ch3cn. I load ch3cn_210.pdb (mecn=loadpdb ch3cn_210.pdb), prep.ch3cn
(loadAmberPrep prep.ch3cn) and frcmod.ch3cn (loadAmberParams frcmod.ch3cn) in
leap and the I try to solvate my protein solvateBox protein mecn 8.0. When I
see the results the protein was not solvated completely, their is some empty
spaces between the solvent. How I could solvate the protein???
 
Anthony


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