I tried to follow correctly your kind suggestion
In leap:
parm10 = loadamberparams parm10.dat
frcmod99SB = loadamberparams frcmod.ff99SB
frcmodionsff99_tip3p = loadamberparams 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
Accordingly, the leap log now tells that:
> addions PROT Na+ 40
Using default radius 1.50 for ion Na+
Adding 40 counter ions to "PROT" using 1A grid
Total solute charge: -40.00 Max atom radius: 2.00
Grid extends from solute vdw + 5.17 to 11.17
Box:
enclosing: -67.51 -49.02 -44.03 67.21 50.89 43.62
sized: 188.49 206.98 211.97
edge: 256.00
Resolution: 1.00 Angstrom.
Tree depth: 8
grid build: 0 sec
Volume = 0.88% of box, grid points 146920
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 66 sec
(Replacing solvent molecule)
Placed Na+ in PROT at (-10.96, -31.34, -3.99)
however, leap log terminates with:
Building topology.
Building atom parameters.
For atom: .R<Na+ 37865>.A<Na+ 1> Could not find vdW (or other) parameters
for type: IP
and so on for all Na+. PROT.parm7 is 0 byte and PROT.rst7 not saved.
I can't understand where I am in error.
Thanks
francesco
On Mon, Jan 12, 2015 at 2:09 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Mon, Jan 12, 2015, Francesco Pietra wrote:
> >
> > In leap ff:
> >
> > parm10 = loadamberparams parm10.dat
> > frcmod99SB = loadamberparams frcmod.ff99SB
> > frcmod.ionsff99_tip3p
>
> You need to use a "loadamberparams" command in the line above.
>
> ...dac
>
>
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Received on Mon Jan 12 2015 - 08:00:03 PST
