If you are using TIP3P water box then and you want JC charges then this
loading frcmod.ionsjc_tip3p will help .
use following command:
loadamberparams frcmod.ionsjc_tip3p
Hope it helps.
On Tue, 1 Mar 2016 at 11:38 Bill Ross <ross.cgl.ucsf.edu> wrote:
> You need to load ion parameters to match your water model. 'could not
> find vdw for Na+'
>
> A look at the parameter file names should make it an easy guess which
> one to load.
>
> Bill
>
> On 3/1/16 3:33 AM, Sreemol G wrote:
> > Hello everyone,
> > I am doing simulation of RNA (23 nucleotides) in amber. I have followed
> the
> > tutorial given in this website(
> > http://ambermd.org/tutorials/basic/tutorial1/section2.htm). While while
> > trying to write prmtop and inpcrd files for neutralised system I
> > encountered the following error I have pasted as snapshot. can anyone
> > please tell me how to rectify it??
> >
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> AMBER.ambermd.org
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>
--
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Tumbi Mohammed Khaled.
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Received on Tue Mar 01 2016 - 04:00:10 PST
