Dear All,
I want to run an antechamber, and tleap for a ligand (it is a silver salt
of carboxylic acid). Further, I want to simulate the single ligand in AMBER
Can you please guide me for setting up the charge and force field in
antechamber and tleap for the ligand of silver salt of carboxylic acid
When I ran an antechamber, using the following command;
~/amber12/bin/antechamber -i lig.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 4
-at gaff -c AM1-BCC -nc 0
I am getting the following message,
For atom[24]:Ag24, the best APS is not zero, bonds involved by this atom
are frozen
For atom[31]:Ag31, the best APS is not zero, bonds involved by this atom
are frozen
For atom[51]:Ag51, the best APS is not zero, bonds involved by this atom
are frozen
For atom[61]:Ag61, the best APS is not zero, bonds involved by this atom
are frozen
When I ran a tleap using the following command;
~/amber14/bin/tleap -s -f tleap.all
the script for tleap as follows:
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 am getting the following error message
Building topology.
Building atom parameters.
For atom: .R<UNK 1>.A<Ag24 24> Could not find vdW (or other) parameters for
type: Ag
For atom: .R<UNK 1>.A<Ag31 31> Could not find vdW (or other) parameters for
type: Ag
For atom: .R<UNK 1>.A<Ag51 51> Could not find vdW (or other) parameters for
type: Ag
For atom: .R<UNK 1>.A<Ag61 61> Could not find vdW (or other) parameters for
type: Ag
Parameter file was not saved.
Please kindly help me to solve those above mentioned errors.
Thanks & regards
*Dr. Ramesh M*
Email: shreeramesh.gmail.com
Mobile: 91 + (0) 9646469938 27+ (0) 844556164
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Received on Wed Feb 04 2015 - 03:30:03 PST
