Dear AMBER of the list,
Thanks for the previous answers, I'm evolving.
I got the little conduct a test using the following procedure to achieve
solvation:
loadamberparams frcmod.iosjc_spce
solvatebox mol SPCBOX 10
loadamberparams frcmod.spce
addions mol Na+ 0
As I understand it when using the above sequence for now
other types of water model is only exchange the term
the corresponding command lines ???
With this in my file I have added two Na+ ions and the simulation box
solvated was created.
Now this is right ????
As do the same to put solvation via implicit solvent ???
Best regards
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2015-09-22 17:44 GMT-03:00 Bill Ross <ross.cgl.ucsf.edu>:
> Try 'list' in leap to see all the molecules. If you have loaded ionic
> files, you will see Na+. That would be the ion to use.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: Marcelo Andrade
> Chagas <andrade.mchagas.gmail.com> </div><div>Date:09/22/2015 12:20 PM
> (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org>
> </div><div>Subject: Re: [AMBER] Addions Na+ </div><div>
> </div>Dear AMBER of the list,
>
> I tried before
>
> addions mol Na 0
>
> that's right?
>
> It needs to load amberparams file for these counter-ions or
> the neutralization is carried out in a single command line, as shown above
> attempted and?
>
> Best regards
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
> 2015-09-22 16:11 GMT-03:00 Bill Ross <ross.cgl.ucsf.edu>:
>
> > In leap try 'help addions'. You didn't specify the ion.
> >
> > Bill
> >
> > <div>-------- Original message --------</div><div>From: Marcelo Andrade
> > Chagas <andrade.mchagas.gmail.com> </div><div>Date:09/22/2015 11:52 AM
> > (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org>
> > </div><div>Subject: [AMBER] Addions Na+ </div><div>
> > </div>Dear AMBER of the list,
> > nando
> > I'm trying to neutralize my system by adding ions such as Na +
> > counter ions,
> > however, using the following
> >
> > In addions mol 0
> >
> > it's not working.
> >
> > How to?
> >
> > It needs to charge amberparams file for these monovalent ions or the
> > addition is a single command line in xleap ???
> >
> > Best regards
> >
> > Marcelo Andrade Chagas, MSc
> > (PhD student)
> > Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> > * http://lqcmm.qui.ufmg.br/
> > Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> > Tel:(31)3409-5776
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> >
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Received on Tue Sep 22 2015 - 14:30:03 PDT
