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> 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:;>
> > 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
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Dec 21 2012 - 02:30:02 PST
