Dear Pengfei and Amber users,
thank you, I tried it but the other error appeared:
> parm bdna30_spc20_18.prmtop
Adding prmtop bdna30_spc20_18.prmtop to parm list. bdna30_spc20_18.prmtop
is the active parm.
> add12_6_4 :Na+,Cl- watermodel SPCE
Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
read from [/home/nick/amber18/dat/leap/parm/lj_1264_pol.dat]. Using default
C4 parameters for water model [SPCE].
***********************************************************
The selected metal ion is Na
The selected metal ion is Cl
Action add12_6_4 failed
LJ12_6_4Error: Could not find parameters for ATOM_TYPE CE
>
____________________________
The solute is DNA.
What could be the next obstacle here?..
So there are parameters for sp2 aromatic carbons (in the purine
nucleobases) missing?
Where would it be possible to find them?
Thank you in advance,
Nick
ср, 3 окт. 2018 г. в 22:26, <amber-request.ambermd.org>:
>
> Message: 1
> Date: Tue, 2 Oct 2018 15:03:46 -0400
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Subject: Re: [AMBER] add12_6_4 Parmed error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <E957BBE0-8442-4444-99E4-C4661A12620B.gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Nick,
>
> I think you had a typo in the command:
>
> .Na+,Cl- should be :Na+,Cl-
>
> Pengfei
>
> > On Oct 2, 2018, at 1:06 PM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
> wrote:
> >
> > Dear Amber users,
> >
> > when I tried to introduce the C LJ parameter for the ions doing
> > add12_6_4 .Na+,Cl- watermodel SPCE (just like in the Amber reflector mail
> > from 4 Feb 2017), an error message appears:
> >
> >> add12_6_4 .Na+,Cl- watermodel SPCE
> > Action add12_6_4 failed
> > UnhandledArgumentWarning: .Na+,Cl-
> >
> > How it should be done correctly? Amber18 and AmberTools18 are in use.
> >
> > Kind regards,
> > Nick
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Oct 04 2018 - 04:30:02 PDT
