Hello:
I am trying to neutralize a protein-metalcomplex of charge -40 (ambertools
14).
In leap ff:
parm10 = loadamberparams parm10.dat
frcmod99SB = loadamberparams frcmod.ff99SB
frcmod.ionsff99_tip3p
frcmodzn = loadamberparams frcmod.MOL.known
frcmodzn = loadamberparams frcmod.MOL.correspondence
frcmodzn = loadamberparams frcmod.added_impr
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
# WAT = TP3
................................
solvatebox PROT TIP3PBOX 12
addions PROT Na+ 40
resulting in error:
For atom: .R<Na+ 37877>.A<Na+ 1> Could not find vdW (or other) parameters
for type: IP
I have already tried different combinations of commands (reading the
ambertool14 manual and the amber forum), also
addions PROT numIons1 0
at no avail.
Thanks for suggestion which files should be loaded.
francesco pietra
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Received on Mon Jan 12 2015 - 02:00:04 PST
