This command didn't work. Again getting same error.. i have used ff14SB
force field and tried to add Na+ ions. ions was successfully added. while
trying to save the topology and coordinate file only I'm getting error. Is
there any problem with chosen force field. What force field i have to
choose for simulating RNA molecule. Could anyone suggest me the best
solution for this
On Tue, Mar 1, 2016 at 5:11 PM, Mohammed Khaled Tumbi <khaledtumbi.gmail.com
> wrote:
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> --
> --------------------------------------------------------
> Tumbi Mohammed Khaled.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
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Received on Tue Mar 01 2016 - 23:00:04 PST
