Adk44: Created page with "Script useful for AMBER9 and NAB users ''path.info'' file can be converted to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' fi..."

2019-05-13T11:07:50Z

Created page with "Script useful for AMBER9 and NAB users ''path.info'' file can be converted to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' fi..."

New page

Script useful for AMBER9 and NAB users

''path.info'' file can be converted to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' file, change privileges of the file:

chmod 755 path2xyz.py

and type:

./path2xyz.py

----
----

#!/usr/bin/env python

import sys
import string

###############################################################
## #
## Edyta Malolepsza #
## David Wales' group, University of Cambridge #
## in case of problems please send email: em427@cam.ac.uk #
## #
###############################################################
##
## transform path.info into path_all.xyz
## ./path2xyz.py
##
###############################################################

prmtop = open("coords.prmtop").read()
f = string.split(prmtop, "\n")

q0 = f.index("%FLAG POINTERS ")
q1 = f.index("%FLAG ATOM_NAME ")
q2 = f.index("%FLAG RESIDUE_LABEL ")
q3 = f.index("%FLAG RESIDUE_POINTER ")

## names of tables are related to names in prmtop file

atomNumber = int(string.split(f[q0+2])[0])

atomName = []
residueLabel = []

an = 0
line = 0
while (an<atomNumber):
for j in range(20):
if (an<atomNumber):
an = an+1
atomName.append(f[q1+2+line][j*4:(j+1)*4].strip())
else:
break
line = line+1

for i in range(q3-q2-2):
for j in range((len(f[q2+2+i])+1)/4):
residueLabel.append(string.strip(f[q2+2+i][j*4:4*(j+1)]))

info = open("path.info").read()
ff = string.split(info, "\n")

xyz = open('path_all.xyz','w')

for i in range(len(ff)/(2+2*atomNumber)):
m = atomNumber*2+2 # number of lines for each stationary points
l = atomNumber+2 # number of lines before coordinates
# xyz.write("%d\n%s %s\n" % (atomNumber, ff[m*i], ff[m*i+1])) # energy and symmetry
xyz.write("%d\n%s\n" % (atomNumber, ff[m*i])) # energy
for j in range(atomNumber):
xyz.write("%-4s %s\n" % (atomName[j], ff[m*i+l+j]))

xyz.write("\n")
xyz.close()

'''Note''': this script works when ''path.info'' file was obtain without NOFRQS keyword. If NOFRQS was used, please, change values of two variables:

m = atomNumber+2 # number of lines for each stationary points
l = 2 # number of lines before coordinates

Path2xyz.py - Revision history

Adk44: Created page with "Script useful for AMBER9 and NAB users ''path.info'' file can be converted to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' fi..."