It still shows the change of the position of protein.
Thank you
Li
On Wed, Jan 15, 2014 at 3:17 PM, Jio M <jiomm.yahoo.com> wrote:
> Hi Li,
>
> > source leaprc.ff99SB
> > prot = loadpdb "reference1.pdb"
> > addions prot Na+ 0
> > set default nocenter on
> > solvateoct prot TIP3PBOX 12.0
> > savepdb prot reference.pdb
>
>
> a vague thingy, try adding ions after water?
> solvateoct prot TIP3PBOX 12.0
>
> addions prot Na+ 0
>
>
>
>
> On Wednesday, January 15, 2014 10:54 PM, 肖立 <xiaoli19871216.gmail.com>
> wrote:
>
> I changed to another computer which have this option so there is no error
> message this time. But I still have that issue when using the solvatebox
> since the position of the protein is changed.
> Thank you
> Li
>
>
> On Wed, Jan 15, 2014 at 2:04 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Wed, Jan 15, 2014, 肖立 wrote:
> >
> > > > > set default nocenter on
> > > > > can't parse nocenter
> >
> > It looks like you need to update your version of AmberTools. Go to
> > $AMBERHOME and re-run the configure script, then type "make install"
> >
> > ...dac
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Li Xiao
> University of California, Irvine
> Email: xiaoli19871216.gmail.com
>
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--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Wed Jan 15 2014 - 15:30:03 PST
