AMBER Archive (2009)

Subject: Re: [AMBER] help with parameters for ions

From: InSuk Joung (i.joung_at_gmail.com)
Date: Tue Jun 02 2009 - 13:14:46 CDT

Hi,
I think the problem is still hidden in "system.lib".

I suggest you trying,

desc Na+.1.1
desc Cl-.1.1

just before you 'saveamberparm' and see the 'Type' of your Na+ and Cl-. Are
they 'Na+' / 'Cl-' or named differently like 'IP' / 'IM'? If the names are
different, you can change either your "system.lib", or the frcmod file
accordingly.

Also note that TIP4P and TIP4PEW are different.

On Tue, Jun 2, 2009 at 1:38 PM, rebeca <rebeca_at_mmb.pcb.ub.es> wrote:

> Hi,thanks for the suggestion, I will change to tip4
> the complete script is this one:
>
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
> loadamberparams frcmod.ionsjc_tip3p
> loadoff system.lib
> addions mol Na+ 30 Cl- 30
> saveamberparm mol ionized.top ionized.crd
> quit
>
> In system.lib I have a library for my system, which is a carbon nanotube
> using the CA carbons included in Amber.
>
> The topology generated ionized.top is exactly the same than that generated
> with the same comands except for the loadamberparams frcmod.ionsjc_tip3p
>
>
> What am I doing wrong?
>
> Rebeca.
>
>
>
> Hi Rebeca,
>
>
> You need to show the complete script of leap. I suspect that your atom
> types are different from the names in the new frcmod file.
>
>
> If your concern is the crystallization of KCl, you'd better use TIP4PEW or
> SPC/E water and their ions. The solubilities of TIP3P-compatible ions are
> also low. We are going to publish the data soon.
>
>
>
> On Tue, 2 Jun 2009 09:46:40 -0400, "David A. Case"
> <case_at_biomaps.rutgers.edu> wrote:
> > On Tue, Jun 02, 2009, rebeca wrote:
> >>
> >> I am doing simulations using a KCl concentration 1M and I have problems
> >> of
> >> crystallization of ions in the simulations. I have seen in the
> literature
> >> that this is normal with Amber parameters for ions.
> >>
> >> I have found a paper
> >> "Determination of Alkali and Monovalent Ion Parameters for Use in
> >> Explicitly Solvated Biomolecular Simulations"
> >> S Joung, Thomas E Cheatham, J. Phys. Chem. B, Vol. 112, No. 30. (1 July
> >> 2008), pp. 9020-9041.
> >> http://www.citeulike.org/user/softsimu/article/3863549
> >
> > Frcmod files for these parameters are in the frcmod_ionsjc_* files in
> > $AMBERHOME/dat/leap/parm. You can use those directly, and also see how
> the
> > frcmod files were created, in case you want to use your own or other
> > parameters.
> >
> > ...hope this helps...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Rebeca García Fandiño
> Molecular Modelling and Bioinformatics Group
> Institut de Reçerca Biomèdica
> Parc Cientific de Barcelona
> 08028 Barcelona
> rebeca_at_mmb.pcb.ub.es
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Best,
InSuk Joung
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