I'm asking as I want to confirm that I have created a solvent box (TIP4PEW)
with the correct # of ions to give a desired ion concentration.
Leap tells me, when I solvate it has added 26249 residues.
The prmtop file (NRES) says that it contains 26852 residues
that tracks with the protein size.
However - when we use ambpdb to write a pdb file, we only see ~6249 water
molecules.
The number of water residue labels (in the prmtop) also matches the number
from leap and the prmtop.
Visualization of the inpcrd/prmtop and the pdb shows that they are the same
size and they directly overlap.
is leap/prmtop simply counting every atom of TIP4PEW as a residue?
Thanks,
JOnathan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 11 2013 - 13:30:02 PDT
