May be there is something wrong with your tleap script or preparation step.
But try with the following tleap.
source leaprc.ff99SB
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor = loadPDB rec.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG LIG.top LIG.crd
receptor = loadPDB rec.pdb
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Na+ 0
solvateBox complex TIP3PBOX 8.0
saveAmberParm complex com_solvated.top com_solvated.crd
savepdb complex com_solvated.pdb
quit
On Tue, Dec 23, 2014 at 1:00 PM, Harmeet Kaur <meet.academia.gmail.com>
wrote:
> Dear Sir,
>
> I am unable to save the parameters of a PDB structure in tleap. The
> structure has an overall -2 charge which was neutralized with Na+.For your
> reference, I am using ff12SB force field in Amber14. It shows the following
> error
>
> Checking Unit.
> Building topology.
> Building atom parameters.
> For atom: .R<Na+ 9351>.A<Na+ 1> Could not find vdW (or other) parameters
> for type: Na+
> For atom: .R<Na+ 9352>.A<Na+ 1> Could not find vdW (or other) parameters
> for type: Na+
> Parameter file was not saved.
>
>
> Kindly guide on how to trouble-shoot the error.
> Thanks a lot
>
> Regards
> Harmeet
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>
--
Thanks & Regards;
Soumendranath Bhakat
Researcher
Homepgae: https://cbiores.wordpress.com/
Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
Past: Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Tue Dec 23 2014 - 03:30:04 PST
