I have a PDB file. I want to duplicate this pdb file automatically instead of doing it manually. For example, if I visualize my PDB, I will find only one structure in (x,y,z). I want to have more copies of my structure. Therefore, I can visualize the PDB, and I can see that there are 9 or 10 copies of the structure in the PDB file, and they are located well close to each other but do not overlap. Then I can solvate without any problem. Is there any Python code or method to do that?
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$\begingroup$ This is tricky. Having one file where the atoms are near one each other normally give errors. $\endgroup$– Camps ♦Apr 24 at 19:31
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$\begingroup$ Not the atoms, I mean the whole structure. For example the distance between each structure 3 A and the position is randomly. But not so far from each other. $\endgroup$– Abd-Elazeem MohamedApr 24 at 19:56
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1$\begingroup$ @Abd-ElazeemMohamed How about using a software called Packmol, where you can put multiple copies of molecules in a box (you need to specify the box size) with a distance tolerance of x ang between any two molecules . $\endgroup$– VasistaApr 24 at 20:10
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$\begingroup$ @Vasista. Yes, I checked and this is what I want. Thanks. You can write it as an answer $\endgroup$– Abd-Elazeem MohamedApr 25 at 9:53
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3 Answers
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You can use Packmol to achieve this. Below is an example script
tolerance 15.0
# The file type of input and output files is PDB
filetype pdb
# The name of the output file
output 20_pq_5jb.pdb
structure polyq_frame_1470.pdb
number 20
inside box 0. 0. 0. 200. 200. 200.
end structure
tolerance 10
structure sim10_frame_1158.pdb
number 5
inside box 0. 0. 0. 200. 200. 200.
end structure
This script can put 20 molecules of type A and five molecules of type B in a box of size 200x200x200.
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This can also be done in VMD using Tcl scripts. The only requirements are that you have a PSF and PDB file for the structure that you want to replicate.
set pdb methanol.pdb # name of pdb file
set psf methanol.psf # name of psf file
set a 3 # repetitions in x-direction
set b 3 # repetitions in y-direction
set c 3 # repetitions in z-direction
set xdist 10 # separation in x-direction
set ydist 10 # separation in y-direction
set zdist 10 # separation in z-direction
set xend [expr $a / 2]
set xstart [expr -1 * $xend]
set yend [expr $b / 2]
set ystart [expr -1 * $yend]
set zend [expr $c / 2]
set zstart [expr -1 * $zend]
set counter 0
# generate the required psf and pdb files
for { set i $xstart } { $i <= $xend } { incr i } {
set xtrans [expr $xdist * $i]
for { set j $ystart } { $j <= $yend } { incr j } {
set ytrans [expr $ydist * $j]
for { set k $zstart } { $k <= $zend } { incr k } {
set ztrans [expr $zdist * $k]
mol load psf $psf
mol addfile $pdb type pdb waitfor all
set sel [atomselect top all] # assuming that your pdb file contains only the molecule that you want to replicate
$sel moveby [vecscale -1 [measure center $sel weight mass]] # moves the molecule to origin
set transvec [list $xtrans $ytrans $ztrans]
$sel moveby $transvec
$sel set segname M$counter
$sel writepdb methanol.$i.$j.$k.pdb
$sel writepsf methanol.$i.$j.$k.psf
incr counter
mol delete all
}
}
}
# merge the generated files
package require topotools 1.6
set molList {}
for { set i $xstart } { $i <= $xend } { incr i } {
for { set j $ystart } { $j <= $yend } { incr j } {
for { set k $zstart } { $k <= $zend } { incr k } {
set mol [mol new methanol.$i.$j.$k.psf waitfor all]
$mol addfile methanol.$i.$j.$k.pdb
lappend molList $mol
}
}
}
set mol [::TopoTools::mergemols $molList]
animate write pdb combined.pdb $mol
animate write psf combined.psf $mol
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This can be achieved with Python. I will demonstrate it with a simple molecule : methanol.
The PDB file of methanol I used looks like this:
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 0.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 -0.278 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 -0.901 1.00 0.00
ATOM 4 H 1 -1.263 0.754 0.600 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 0.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 0.137 1.00 0.00
TER 6 1
END
Let us initialize some paths and variables:
input_pdb_path = 'input/methanol.pdb'
output_pdb_with_repeated_mols = 'output/methanol_repeated.pdb'
n_mols = 10
Let us now read the PDB which we wish to repeat.
with open(input_pdb_path, 'r') as in_file:
data = in_file.read()
A new PDB will be created at the output path defined in the initialization. Since you require that the molecules are not overlapping, let us translate them in the z axis by 1 unit from each other.
This is achieved by the following function:
def translate_mol_in_z_axis(data, translation_dist):
pattern = r'-?[\d]*[.][\d]+' # This pattern will capture any numbers with decimals digits
edited_lines = []
n_decimal_places =3
for line in data.split('\n'):
numeric_info = [(m.start(0), m.end(0), m.group(0)) for m in re.finditer(pattern, line)]
if numeric_info:
x_coord_info = numeric_info[0]
y_coord_info = numeric_info[1]
z_coord_info = numeric_info[2]
z_coord_start_idx= z_coord_info[0]
z_coord_end_idx= z_coord_info[1]
z_coord_val = z_coord_info[2]
line_edited = line[:z_coord_start_idx] + str(round(float(z_coord_val)+translation_dist, n_decimal_places)) + line[z_coord_end_idx+1:]
else:
line_edited = line
edited_lines.append(line_edited)
edited_mol_pdb = '\n'.join(edited_lines)
return edited_mol_pdb
Let us now replicate the molecules in a new output file:
with open(output_pdb_with_repeated_mols, 'w') as out_file:
for i in range(n_mols):
translation_dist = i
out_file.write('\n\n')
translated_mol_data = translate_mol_in_z_axis(data, translation_dist)
out_file.write(translated_mol_data)
When the output PDB is viewed in a software like PyMOL, you will see that the molecules are stacked with 1 unit distance in the z axis like this:
The output file will look like this:
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 0.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 -0.278 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 -0.901 1.00 0.00
ATOM 4 H 1 -1.263 0.754 0.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 0.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 0.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 1.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 0.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 0.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 1.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 1.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 1.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 2.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 1.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 1.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 2.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 2.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 2.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 3.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 2.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 2.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 3.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 3.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 3.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 4.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 3.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 3.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 4.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 4.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 4.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 5.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 4.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 4.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 5.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 5.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 5.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 6.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 5.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 5.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 6.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 6.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 6.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 7.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 6.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 6.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 7.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 7.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 7.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 8.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 7.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 7.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 8.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 8.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 8.137 1.00 0.00
TER 6 1
END
COMPND METHANOL
ATOM 1 C 1 -0.748 -0.015 9.024 1.00 0.00
ATOM 2 O 1 0.558 0.420 8.722 1.00 0.00
ATOM 3 H 1 -1.293 -0.202 8.099 1.00 0.00
ATOM 4 H 1 -1.263 0.754 9.6 1.00 0.00
ATOM 5 H 1 -0.699 -0.934 9.609 1.00 0.00
ATOM 6 H 1 0.716 1.404 9.137 1.00 0.00
TER 6 1
END
answered Apr 25 at 10:03
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$\begingroup$ @Abd-ElazeemMohamed if my answer helped you, then please consider upvoting $\endgroup$ Apr 25 at 16:01