Hii;;
I believe you ran antechamber and frcmd properly. Just try with this tleap
script. I believe your have Na+ as a counter ion.
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
Best,
S.Bhakat
On Fri, May 23, 2014 at 12:38 AM, Lara rajam <lara.4884.gmail.com> wrote:
> Dear Amber
>
> I have gone through the amber advanced tutorial
> http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
>
> I followed the same to the molecules of my interest ( protein and ligand
> complex )
>
> I have a problem in generating the initial prmtop files
>
> I followed the steps
>
> loading the frcmod of ligand
> loading protein
> combining the protein and ligand
>
> set default PBRadii mbondi2
>
> saved the parmtop and inpcrd for the protein , ligand and complex
>
> The complex need counter ion so i added Na+ to neutralize the charge and
> then solvated with the box of 12 A
>
> when i attempt to save the prmtop file it said error
>
> For atom: .R<Na+ 114>.A<Na+ 1> Could not find vdW (or other) parameters for
> type: Na+
>
> how can i fix this to generate the prmtop file so that i can use these
> files for later mmpbsa calculations
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu May 22 2014 - 13:00:02 PDT
