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AMBER, TIP4P-Ew and NAMD

Consider this untested. Leap script:

source leaprc.ff99SBildn
loadamberparams frcmod.tip4pew
loadamberparams frcmod.ionsjc_tip4pew
loadoff tip4pewbox.off
WAT = T4E 
set default FlexibleWater on
lyta = loadPdb aligned.pdb
check lyta
solvateBox lyta TIP4PEWBOX 7.0 iso
addions lyta Na+ 2
saveAmberParm lyta lyta.prmtop lyta.crd
savepdb lyta lyta.pdb
quit 

and in the namd script add

waterModel tip4
research/howto/amber99sb-ildn_tip4p-ew_and_namd.txt · Last modified: 2011/07/14 10:57 (external edit)