ptraj is the optimal tool for that. You need to write a small input file:
trajin md.crd
distance DIST .atom_number1 .atom_number2 out ptraj.out
go
then you run ptraj:
>ptraj prmtop ptraj.inp
where prmtop is your topology file, ptraj.inp and the 3-line input file.
and here comes everything as python script, in case you want to do it
several times:
mdist.py:
----------------
from sys import *
import commands
def ptraj_distance(f_top, f_crd, atom1, atom2):
"""call ptraj and dump 2 column list with frame
vs. interatom-distance"""
# form ptraj input file
ptraj_input = open('ptraj.inp','w')
ptraj_input.write("""trajin %s
distance DIST .%d .%d out ptraj.out
go
""" % (f_crd, atom1, atom2))
ptraj_input.close()
try:
print 'calling ptraj...please wait'
print commands.getoutput('ptraj %s ptraj.inp' % f_top)
print commands.getoutput('rm ptraj.inp')
except:
print "Error while creating ptraj input file."
#######################
# MAIN
#######################
if __name__ == '__main__':
if len (argv) < 5: # at least 4 arguments
print """Syntax: mdist |prmtop| |mdcrd| |atom1| |atom2|"""
else:
ptraj_distance(argv[1], argv[2], int(argv[3]), int(argv[4]))
--------------
That's it. Just call it "python mdist.py prmtop myMd.crd 23 195".
Ciao
Raik
On Thu, 11 Apr 2002, Francois Dupradeau wrote:
|Dear All,
|
|I would like to follow distances between 2 atoms during MD runs. Which
|AMBER program should I use and could you give me advice on the
|corresponding input ?
|
|I would like to get y=f(x) data to display them in graphical program....
|
|Thanks, Regards, Francois
|
|
=====================================================
Raik Grünberg | Bioinformatique Structurale
| Institut Pasteur
| 25-28 rue du docteur Roux
raik_at_pasteur.fr | 75015 Paris
Tel: +33/1.45.68.87.37 | France
-----------------------------------------------------
http://www.raiks.de/contact.html
=====================================================
Received on Thu Apr 11 2002 - 05:49:16 PDT
