AMBER Archive (2009)

Subject: Re: [AMBER] errors when add ions

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu May 21 2009 - 07:23:08 CDT

On Thu, May 21, 2009, zgong.hust wrote:

> I would like to add magnesium to the RNA molecule before perform the MD simulations, However, when I use the tleap to add magnesium ions, some error happened
> the software vision is AMBER 9, and the force filed is leaprc.rna.ff98
>
> Here is the command
>
> model=loadpdb xxx.pdb
> addions MG2 30
> solvatebox model TIP3PBOX 8.0
>
> when I want to save the prmtop and inpcrd files, some error happened
>
> For atom: .R<MG2 84>.A<MG 1> Could not find type: MG

Looks like parm98.dat does not define the Lennard-Jones parameters for MG.
Find the following line in parm99.dat:

  MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted)

and put it with the other ions near the bottom of parm98.dat.

Be aware that using a simple point charge sphere for a divalent ion is a real
stretch. You should not expect quantitative results for energies. You might
also want to think about the use of ff98: it is no longer of the list of
"recommeded" force fields, and ff99 is certainly more widely used. Others on
the list know more than I do about this.

...dac

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