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
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 20 2012 - 07:00:02 PST
