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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Received on Thu Feb 05 2015 - 01:30:02 PST
