It seems that there is no standard parameter specified for the ions
with tip4p-fb water model as this water model is newly developed
Possibly to use the parameter in "frcmod.ionsjc_tip4pew" as the roughly
parameter for the ions in tip4p-fb water model,
I'm sorry not to help much,
jing
On Thu, Jan 5, 2017 at 7:44 PM, Samaneh Ghassabi Kondalaji <
saghassabikondalaji.mix.wvu.edu> wrote:
> Dear Amber developers and users
> I am attempting to use tip4pfb water model to solvate a peptide.
> Initially I sourced the leaprc.protein.ff14SB file in addition to loading
> solvents.lib, frcmod.tip4pfb and atomic_ions.lib files. After solvating the
> peptide in FB4BOX, using the addions (or addions2) I added 2 Na+ ions
> without any errors (the Na+ exists in Unit list). However, when I try to
> save the prmtop and inpcrd files, I get this error (leap.log file is
> attached to this E-mail):
> *For atom: .R<Na+ 520>.A<Na+ 1> Could not find vdW (or other) parameters
> for type: Na+*
> Now, I understand that I need to source ion parameters using files such
> as leaprc.water.tip4pewFB4 and frcmod.ionsjc_tip4pewFB4 for FB4BOX water
> model, except that these files do not exist. Any suggestions on how I can
> find these parameters would be greatly appreciated.
>
> Best Regards
> samaneh
>
> P.S. The system is a peptide (ACE LYS NME) with overall charge state of +3
> in water. The error message does not appear when I use tip3fb water model
> with related force field files.
>
>
> --
> *Samaneh ghassabi kondalaji*
> *PhD student in Chemistry*
> *555 CRL, Chemistry department*
> *West Virginia University *
> *Morgantown, USA*
>
> *E-mail: **saghassabikondalaji.mix.wvu.edu*
> <saghassabikondalaji.mix.wvu.edu>
>
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Received on Thu Jan 05 2017 - 14:00:02 PST
