Hi Kenneth,
Thank you for you email and advise.
I have used the command you suggested:
loadamberparms frcmod.ionsjc_tip3p
Unfortunately xleaps responds with error:
ERROR: syntax error
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
On Sun, May 10, 2015 at 9:35 PM, Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> 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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> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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> here could not dream of heaven?
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Received on Sun May 10 2015 - 12:00:03 PDT
