Hi Bill,
Thanks . yes my system has a protein + ligand (HQN) + 6 fatty acid molecules (MYR1-6) bound to the protein.
--------------------------
complex = combine {protein HQN MYR1 MYR2 MYR3 MYR4 MYR5 MYR6}
charge complex
addions complex Na+ 0
solvateOct complex TIP3PBOX 8.0
saveamberparm complex hqn0101cx2.prmtop hqn0101cx2.inpcrd
----------------------------------------
solvatebox works fine with the same system. But as the protein is quite large, it adds up more than ~20000
water molecules. I want to reduce the numbers as much as possible.
I am also wondering how to mention the position argument for solvateCap command,
if I want to consider the center of the whole system. I tried as follows:
solvateCap complex TIP3PBOX complex 12.0
but it doesn't seem to understand the #3 position argument.
Thanks for your time and suggestions.
Senthil
> I visually inspected the system and side chain of one residue is almost
> out of the box.
Do you have multiple solute molecules? Having authored solvateOct in
the remote past, this is the only thing I can think of that might
lead to atoms not being considered in drawing the box. Even then, it
seems like there might be something unusual in your setup, since
as mentioned the code has been around for a while without this arising.
Bill
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Received on Tue Nov 08 2011 - 15:00:03 PST
