I think you need to load one more file which is loadamberparams
frcmod.ionsjc_tip3p in tleap.
Regards,
Pradeep Pant
On Mon, Jan 12, 2015 at 3:27 PM, Francesco Pietra <chiendarret.gmail.com>
wrote:
> 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 Tue Jan 13 2015 - 01:00:02 PST
