Adk44: Created page with "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..."

2019-05-13T10:58:06Z

Created page with "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..."

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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

----
----

#!/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))

Path2pdb.py - Revision history

Adk44: Created page with "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..."