Re: [AMBER] parameters for type: Cl-

From: David A Case <>
Date: Sun, 10 May 2015 17:08:53 -0400

On Sun, May 10, 2015, Michael Shokhen wrote:
> What is a correct xleap command for accounting Cl-
> counter ions that will avoid the error?

Please see Chapter 3.9 ("Ions") for details here. Basically, you need to
choose ion parameters that match the water model you are using. Since you
chose TIP3P, you just need to include the following line:

  loadAmberParmams frcmod.ionsjc_tip3p (the first choice in the list)

> *xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB*
> *>set default PBRadii mbondi2*
> *>p1 = loadpdb hp.pdb*
> *>addions p1 Cl- 0*
> *>solvateoct p1 TIP3PBOX 15*
> *>saveamberparm p1 hp.prmtop hp.inpcrd*
> *For atom: .R<Cl- 153>.A<Cl- 1> Could not find vdW (or other) parameters
> for type: Cl-*

[An aside: the current Ions chapter makes things look *really* complex. But
in fact, for alkali or halide ions, you just need to choose one of the
frcmod.ionsjc_* files, depending on which water model you are using.]

[Second aside: The "correct" pdb residue and atom name for chloride is "CL",
and there are advantages to following the standard. We still support the old
Amber names, like "Cl-", but this in only for backwards compatibility. It was
a mistake to have just made up our own names.]


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Received on Sun May 10 2015 - 14:30:02 PDT
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