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

From: Jio M <jiomm.yahoo.com>
Date: Wed, 15 Jan 2014 15:17:27 -0800 (PST)

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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>



-- 
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Wed Jan 15 2014 - 15:30:02 PST
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