Path2pdb.py

Script useful for AMBER9 and NAB users

path.info file can be easy converted to the PDB format using Python program presented below. PDB file can be loaded to VMD and you can visualize your path. Because of simplicity all residues have the same name ALA therefore better is to load topology file and as next the PDB file.

To do this save the code in path2pdb.py file, change privileges of this file:

chmod 755 path2pdb.py

and type:

./path2pdb.py

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#!/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.pdb
## ./path2pdb.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.pdb','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
    mm = 1                 # number of residue
    for j in range(atomNumber):
        x = float(string.split(ff[m*i+l+j])[0])
        y = float(string.split(ff[m*i+l+j])[1])
        z = float(string.split(ff[m*i+l+j])[2])
        if (atomName[j]=='N' and atomName[j+1]=='H'):
            mm = mm+1
        else:
            xyz.write("%4s%7d %-4s %4s%5d%12.3f%8.3f%8.3f\n" % ('ATOM', j+1, atomName[j], 'ALA', mm, x, y, z))
    xyz.write("END\n")

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

Bug fix: There was bug when used with path.info output of A9OPTIM. To fix, edit if-else statement as below:

       z = float(string.split(ff[m*i+l+j])[2])
       # bug fix on 12 Jan 2012. ss2029  
       if (atomName[j]=='N' and atomName[j+1]=='H'):
           mm = mm+1
       xyz.write("%4s%7d %-4s %4s%5d%12.3f%8.3f%8.3f\n" % ('ATOM', j+1, atomName[j], 'ALA', mm, x, y, z))