AMBER Archive (2005)

Subject: Re: AMBER: How can I read parm99.dat file?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri May 06 2005 - 15:08:59 CDT

> Does your answer mean if I make only library file for I-, and don't make
> frcmod file, the parameters, R = 2.35 and EDEP = 0.40, will be used
> automatically?

Yes, if you make the atom type 'I'. You could choose another type
name to avoid using the params, but would have to define mass and
vdw in a frcmod.

> In the parm file, is "IM" data for Cl-(Chloride ion)?

I believe so..

> Cl is for Cl(Cholorine)?

Possibly also Cl-; check the vdw params to see if they match IM.

Bill
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