source leaprc.ff99SB
prot = loadpdb "reference1.pdb"
addions prot Na+ 0
set default nocenter on
solvateoct prot TIP3PBOX 12.0
savepdb prot reference.pdb
Thanks a lot!
Li
On Wed, Jan 15, 2014 at 12:21 PM, Kevin Hauser <84hauser.gmail.com> wrote:
> Hi Li,
>
> Could you send us your exact leap script? Is your AmberTools all up to
> date?
>
> Kevin
>
>
> On Wed, Jan 15, 2014 at 2:51 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
>
> > Thank you. But it shows this error message:
> > set default nocenter on
> > can't parse nocenter
> > usage: set <container> <parameter> <object>
> > or: set default <parameter> <value>
> >
> > How to make it right?
> > Li
> >
> >
> > On Wed, Jan 15, 2014 at 11:29 AM, James Maier <jimbo.maier.gmail.com>
> > wrote:
> >
> > > Try 'set default nocenter on'
> > >
> > > James
> > >
> > >
> > > On Wed, Jan 15, 2014 at 2:24 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
> > >
> > > > Hi, all:
> > > > I face a problem when adding water in tleap.
> > > > After typing
> > > > solvateoct prot TIP3PBOX 12.0
> > > > savepdb prot reference.pdb
> > > > The protein can't remain the original position.
> > > > Could anyone tells me if there is anyway I can add water while keep
> > the
> > > > protein's original position?
> > > > Thanks a lot!
> > > >
> > > > --
> > > > Li Xiao
> > > > University of California, Irvine
> > > > Email: xiaoli19871216.gmail.com
> > > > _______________________________________________
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> > > >
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Li Xiao
> > University of California, Irvine
> > Email: xiaoli19871216.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -- - -
> HK
>
>
> ════════════════════════════════════════════
> Kevin E. Hauser, Ph.D. Candidate
> NRSA Fellow, National Institutes of Health
> Carlos Simmerling Laboratory
> Miguel Garcia-Diaz Laboratory
> 100 Laufer Center for Physical and Quantitative Biology
> Stony Brook, New York 11794-5252
> Phone: (631) 632.5394 Email: 84hauser.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 - 14:00:02 PST
