Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap

From: Kevin Hauser <84hauser.gmail.com>
Date: Wed, 15 Jan 2014 22:07:52 -0500

Hi Li,

Can you post your leap.log, please? How many atoms is your
"reference1.pdb"? And just to be clear, the actual coordinates of the atoms
in reference1.pdb are different from those printed by leap, right? It's not
that VMD has zoomed out since your system is much larger now, right?

Kevin


On Wed, Jan 15, 2014 at 6:24 PM, v <xiaoli19871216.gmail.com> wrote:

> 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, v <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, v 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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> > http://lists.ambermd.org/mailman/listinfo/amber
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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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> 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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Received on Wed Jan 15 2014 - 19:30:02 PST
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