# enter pdb file name
fpdb="mypdb"
fpsf="mypsf"

fob=open("runme.tcl","w")
f1=fob.write

# enter atomname, atomtype, atomcharge
# in any order, any where inside cg
# example: HW1 is resname in pdb file, HW is the atomtype name i wish to have and 0.464116 is the charge

cg=[['HW1','HW','0.464116'],
['HW2','HW','0.464116'],
['OW1','OW','-0.928231'],
['Cs1','CsI','-0.650000'],
['NS1','NS','1.000000'],
['OS1','OS','0.950000'],
['OS2','OS','-0.650000'],
['OS3','OS','-0.650000'],
['C','C','0.000000']]

f1("mol new %s.pdb\n\
mol reanalyze top\n\
mol bondsrecalc top\n\
topo guessbonds\n\
topo guessangles\n\
topo guessdihedrals\n\
topo retypebonds\n\n" %(fpdb))

print "Please match the following:"

for i in range(len(cg)):
        var="s"+str(i)
        f1("set %s [atomselect top {name %s}]\n" %(var,cg[i][0]))
        f1("$%s set type %s\n" %(var,cg[i][1]))
        f1("$%s set charge %s\n\n" %(var,cg[i][2]))
        print "%s %s %s" %(cg[i][0],cg[i][1],cg[i][2])
        
f1("animate write psf %s.psf" %fpsf)

print "runme.tcl file generated. Run it in vmd!!"
fob.close()