Sir i have used Amber 12,
and the tleap input is befor loading the pdb file
tleap
> source leaprc.gaff
>source leaprc.ff10
>source leaprc.ff12SB
sir i have tried in Google solution but i can't have the solution
On Tue, May 24, 2016 at 10:08 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Please be more specific
>
> 1. give us exact tleap input you use
> 2. which AmberTools version?
> 3. And have you tried solution in first 4 post in google yet?
>
> https://www.google.com/search?q=Could+not+find+vdW+%28or+other%29+parameters+for+type%3A+Na%2B&ie=utf-8&oe=utf-8
>
> cheers
>
> Hai
>
> On Tue, May 24, 2016 at 12:21 PM, Vishal Nemaysh <
> vishal.bioinfotech.gmail.com> wrote:
>
> > Respected Sir,
> >
> > I have faced the following problem when i save the .prmtop and .inpcrd
> file
> > the appeared massege is as follow:
> >
> > > saveamberparm b neelamber_w_ions.prmtop neelamber_w_ions.inpcrd
> > Checking Unit.
> > Building topology.
> > Building atom parameters.
> > For atom: .R<Na+ 364>.A<Na+ 1> Could not find vdW (or other) parameters
> for
> > type: Na+
> > For atom: .R<Na+ 365>.A<Na+ 1> Could not find vdW (or other) parameters
> for
> > type: Na+
> > For atom: .R<Na+ 366>.A<Na+ 1> Could not find vdW (or other) parameters
> for
> > type: Na+
> > For atom: .R<Na+ 367>.A<Na+ 1> Could not find vdW (or other) parameters
> for
> > type: Na+
> > For atom: .R<Na+ 368>.A<Na+ 1> Could not find vdW (or other) parameters
> for
> > type: Na+
> > Parameter file was not saved.
> >
> > the pdb file is attached herewith
> > --
> > Vishal Nemaysh
> > Research Scholar,
> > Neuropharmaceutical Chemistry lab.,
> > Dr. B. R. Ambedkar Center for Biomedical Research,
> > University of Delhi, Delhi-110007
> > Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> > Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
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>
--
Vishal Nemaysh
Research Scholar,
Neuropharmaceutical Chemistry lab.,
Dr. B. R. Ambedkar Center for Biomedical Research,
University of Delhi, Delhi-110007
Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
Phone: 91-11-27662778 Mobile: 91+8447581401, 91+9650736653
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Received on Tue May 24 2016 - 10:30:02 PDT
