Micheal,
The general form of the command you're likely looking for is-
loadamberparms frcmod.ionsjc_tip3p
Usually, you want to load it before you add in your counterions. Note that
the above forcefield is just the one that I default to- I believe there's a
number of forcefields for different situations.
Best,
Kenneth
On Sunday, May 10, 2015, Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
> Dear Amber list members,
>
> I have on ubuntu linux amber14 and amber tools 15 installed.
> Preparing protein by xleap I have faced the error message
> (see details below).
>
> What is a correct xleap command for accounting Cl-
>
> counter ions that will avoid the error?
>
>
> Thank you,
> Michael
>
>
> *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*
>
>
>
>
> *Checking Unit.*
>
> *Building topology.*
>
>
> *Building atom parameters.*
>
> *For atom: .R<Cl- 153>.A<Cl- 1> Could not find vdW (or other) parameters
> for type: Cl-*
>
> *Parameter file was not saved.*
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: michael.shokhen.gmail.com <javascript:;>
> email: shokhen.mail.biu.ac.il <javascript:;>
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>
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Received on Sun May 10 2015 - 12:00:02 PDT
