Extractedmin2pdb.py

Scripts useful for AMBER9 and NAB users

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If you extracted minima from points.min file and you have extractedmin file you can use Python program presented below to convert this file to PDB format. Save the code in extractedmin2pdb.py file, next change privileges of this file:

chmod 755 extractedmin2pdb.py

and type:

./extractedmin2pdb.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 extractedmin into extractedmin.pdb
## ./extractedmin2pdb.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("extractedmin").read()
ff = string.split(info, "\n")

xyz = open('extractedmin.pdb','w')

for i in range(len(ff)/(atomNumber)):
    mm = 1
    for j in range(atomNumber):
        x = float(string.split(ff[atomNumber*i+j])[0])
        y = float(string.split(ff[atomNumber*i+j])[1])
        z = float(string.split(ff[atomNumber*i+j])[2])
        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], residueLabel[mm-1], mm, x, y, z))
        else:
            xyz.write("%4s%7d %-4s %-4s%5d%12.3f%8.3f%8.3f\n" % ('ATOM', j+1, atomName[j], residueLabel[mm-1], mm, x, y, z))

    xyz.write("END\n")

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