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
>
> _______________________________________________
> AMBER mailing list
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 15 2014 - 15:30:02 PST
