AMBER Archive (2004)

Subject: AMBER: ptraj parser

From: Thomas C. Bishop (
Date: Wed Apr 07 2004 - 10:01:15 CDT

Dear Amber,

Please note that I observe some strange behavior for the ptraj parser.
Attached is the ptraj script I use. (yes I'm sure there are better ways
to construct the script)

I have found that if the file name begins with the text "nofit"
then the parser mistakenly picks up this file name as the "nofit" key
word and scrambles the rest of the line.

The easy solution is to name the files "sys.nofit.rms" or "notfit" or
anything that does not begin with "nofit"!

Just a friendly reminder to all ptraj users
"Note that the current parser is not very sophisticated." (amber
manuals, 6,7,8)

Now can anyone suggest how I select only the heavy atoms for a limited
number of residues?
:1-50@~H* applies the "NOT" to the residue selection AND atom selection.
:1-50_at_C*,N*,O*,S*,P* should pick up all non-hydrogens for resids 1-50
right? or does this miss some atoms?
Other suggestions for getting the rms that I want?


************************** ptraj script ****************
set BAC = "@CA,C,N,O"
set SYS = ":1-105"
set PRO = ":1-76"
set DNA = ":77-105"
set NA = ":106-116"
set CL = ":117-128"
set PARM = "nowat.parm"
set TRAJ1 = "nowat.eq1-2.dcd"
set BASEDIR = "/data/bishop/sims/"
setenv AMBERHOME /usr/local/amber/amber8

$AMBERHOME/exe/ptraj $PARM << EOF
trajin nowat.eq1-2.dcd 1 5 1
rms first mass out nofit.sys.rms $SYS nofit
rms first mass out fit.sys.rms $SYS
rms first mass out $PRO
rms first mass out fit.probac.rms $PRO$BAC


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