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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Received on Wed Feb 04 2015 - 04:30:02 PST
