I think the suggestion was to _not_ use antechamber for this problem.
It hasn't been designed for this. The given alternatives were
literature search or try using the MCPB tool.
On Wed, 4 Feb 2015 04:25:24 -0800
Shreeramesh <shreeramesh.gmail.com> wrote:
> Dear Sir,
>
> Can you please elaborate more about handling of silver ion in
> antechamber by hand
>
> I am not clear about handling by hand
>
> Thanks & regards
>
> *Dr. Ramesh M*
> Email: shreeramesh.gmail.com
> Mobile: 91 + (0) 9646469938 27+ (0) 844556164
>
>
>
> On Wed, Feb 4, 2015 at 3:52 AM, Hannes Loeffler
> <Hannes.Loeffler.stfc.ac.uk> wrote:
>
> > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
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> >
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Received on Wed Feb 04 2015 - 06:00:06 PST
