Dear all,
In tutorial A13 "Simulation of a protein crystal", three successive commands to add acetate, ammonium and water molecules are
CPrograms/AddToBox -c x1AHO.pdb -a Acetate.pdb -na 7 -o xa1AHO.pdb -P 4143 -RP 3.0 -RW 6.0 -G 0.2 -V 1 -X 45.9 -Y 40.7 -Z 30.1 -al 90.0 -bt 90.0 -gm 90.0
CPrograms/AddToBox -c xa1AHO.pdb -a Ammonium.pdb -na 3 -o xm1AHO.pdb -P 4192 -RP 3.0 -RW 6.0 -G 0.2 -V 1 -X 45.9 -Y 40.7 -Z 30.1 -al 90.0 -bt 90.0 -gm 90.0
CPrograms/AddToBox -c xm1AHO.pdb -a spce.pdb -na 179 -o solv1AHO.pdb -P 4192 -RP 3.0 -RW 3.0 -G 0.2 -V 1 -X 45.9 -Y 40.7 -Z 30.1 -al 90.0 -bt 90.0 -gm 90.0
When adding water molecules to the system, only 4192 atoms are taken as solute, with ammonium excluded. I think it should be 4207 in the third command.
Otherwise, I am afraid the newly added water molecules might be too close to ammonium molecules added by the second command.
--------------
Ye MEI
2010-10-15
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Received on Thu Oct 14 2010 - 21:30:03 PDT
