Hi,
Jason Swails has a nice installation guide for Macs that you may find
useful:
http://jswails.wikidot.com/mac-os-x
-Dan
On Friday, December 21, 2012, HM wrote:
> Thanks Daniel,
> I will try this up. In my lab, I have all Mac systems and I am more used to
> use AMBER on linux OS, so was bit lazy to install AMBER on Mac ( as I fail
> all the time with little effort). :-(
> But I will do it now.
>
> Thanks
> HM
>
> On Thu, Dec 20, 2012 at 3:49 PM, Daniel Roe <daniel.r.roe.gmail.com<javascript:;>>
> wrote:
>
> > Hi,
> >
> > Just download and install AmberTools12 (it's free,
> > http://ambermd.org/AmberTools-get.html) and use cpptraj from there. The
> > script you posted seems fine. Let me know if you have any more issues.
> >
> > -Dan
> >
> > On Thursday, December 20, 2012, HM wrote:
> >
> > > Hi All,
> > > I want to use cpptraj module in AMBER10 or 11 ( I do not have AMBER12
> > > installed at my university server :-( ). I was just wondering how can I
> > use
> > > cpptraj to generate the new topology file.
> > >
> > > Actually I want to strip the water and ions from my trajectories (mdcrd
> > > format) and I want to save new coordinate file and topology file
> (without
> > > water and ions). In ptraj i can generate new coordinate file, but i can
> > > not generate new topology file. I came across this discussion (
> > > http://archive.ambermd.org/201212/0067.html) and came to know that it
> is
> > > possible in cpptraj.
> > >
> > > Kindly let me know how to proceed further.
> > >
> > > I am using following script:
> > >
> > > trajin eq1.mdcrd 1 200 1
> > > strip :WAT outprefix strip
> > > autoimage
> > > rms first out rmsd.out .CA,C,N
> > > trajout protein_prod_centered.mdcrd nobox
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;> <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-9119 (Fax)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Dec 21 2012 - 05:30:02 PST
