You need to load the frcmod file for the ions - the set that is compatible
with the water model you use.
So in your case, add the following to your leap-script:
loadamberparams frcmod.ionsjc_tip3p
--Marc
On 5 February 2015 at 09:18, Shreeramesh <shreeramesh.gmail.com> wrote:
> Dear All,
>
> I ran a tleap for the ligand, it is an anioc carboxylate molecule
>
> The script of tleap as follows. It includes Na+ ion to nuetralize the
> carboxylate anion
>
> source leaprc.ff12SB
> source leaprc.gaff
> LIG = loadmol2 LIG.mol2
> saveAmberParm LIG LIG.top LIG.crd
> loadamberparams LIG.frcmod
> check LIG
> set default PBRadii mbondi2
> saveAmberParm LIG LIG.top LIG.crd
> charge LIG
> addIons2 LIG Na+ 0
> solvateBox LIG TIP3PBOX 10.0
> saveAmberParm LIG LIG_solvated.top LIG_solvated.crd
> savepdb LIG LIG_solvated.pdb
> quit
>
>
> I got the following error message and I request you to kindly help me to
> solve it
>
> Error
>
> Building atom parameters.
> For atom: .R<Na+ 2>.A<Na+ 1> Could not find vdW (or other) parameters for
> type: Na+
> For atom: .R<Na+ 3>.A<Na+ 1> Could not find vdW (or other) parameters for
> type: Na+
> Parameter file was not saved.
>
>
> Please kindly suggest me a suitable source file for the counter ion like
> Na+ or Cl- or Ag+ ion, etc.
>
>
>
>
> Thanks & regards
>
> *Dr. Ramesh M*
> Email: shreeramesh.gmail.com
> Mobile: 91 + (0) 9646469938 27+ (0) 844556164
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>
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Received on Thu Feb 05 2015 - 01:30:03 PST
