Based on your error messages, my guess is that you didn't load any ion
parameters. Since you are using an older version of Amber, you will
want to load ion parameters for whatever water model you are using via
the 'loadamberparams' command, e.g.
loadamberparams fcrmod.ionsjc_tip3p
Hope this helps,
-Dan
On Tue, May 24, 2016 at 11:02 AM, Vishal Nemaysh
<vishal.bioinfotech.gmail.com> wrote:
> 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
>> >
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> 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
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 24 2016 - 10:30:03 PDT
