Maybe you follow the advice given to you earlier,
http://archive.ambermd.org/201501/0444.html ?
On Wed, 4 Feb 2015 03:06:06 -0800
Shreeramesh <shreeramesh.gmail.com> wrote:
> 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 - 04:00:03 PST
