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
Received on Thu Dec 20 2012 - 07:00:04 PST
