Read a dmol DCAR file putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop reading on End-of-file, or 'END' line.
Here is a sample file:
!MSI archive 2 PBC=OFF DMol output .car file; Hirshfeld partial charges !date C1 0.023686931 0.012495107 -0.007829269 dmol 1 C 0.0354 1 C2 2.843215911 0.013994655 0.001164353 dmol 1 C -0.0723 2 C3 2.827832482 2.478733396 0.013675318 dmol 1 C -0.0518 3 C4 0.051153183 2.485086901 -0.037928336 dmol 1 C -0.0582 4 C5 0.725787474 1.250353341 -0.001539732 dmol 1 C -0.0162 5 C6 0.739853552 -1.167748028 -0.020982015 dmol 1 C -0.0806 6 C7 2.142159249 -1.166479489 -0.026115009 dmol 1 C -0.0591 7 C8 2.150693385 1.241655457 0.012056303 dmol 1 C -0.0055 8 C9 2.145387402 3.671603031 -0.007541485 dmol 1 C -0.0574 9 C10 0.739696008 3.675868114 -0.039536914 dmol 1 C -0.0587 10 N1 -1.363420688 0.016179865 -0.062974898 dmol 1 N -0.1832 11 H1 3.940376021 0.028288071 0.006272796 dmol 1 H 0.0493 12 end end
Read a Brookhaven file putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop reading on End-of-file, or 'END' line, or line with just a ".".
Here is a sample file:
ATOM 19 HN THR 2 15.386 10.901 4.600 ATOM 20 HOG THR 2 14.161 9.481 4.420 ATOM 21 N CYS 3 13.507 11.238 8.398 ATOM 22 CA CYS 3 13.659 10.715 9.763 ATOM 23 C CYS 3 12.265 10.443 10.307 HETATM 99 FE XXX 4 33.265 10.443 10.307 ATOM OT OME 52 -16.009 30.871 -13.037 -0.543 HETATM CU+2CU 152 -20.577 2.601 -14.587 2.000 HETATM ZN+2ZN 152 -17.911 1.372 -19.974 2.000 END
These charge values are non-standard and are not genuine PDB. They are optional.
Read a DMOL COORD file, putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop reading on End-of-file, or 'END' line, or line with just a ".".
Here is a sample file:
6 0.023686931 0.012495107 -0.007829269
6 2.843215911 0.013994655 0.001164353
6 2.827832482 2.478733396 0.013675318
6 0.051153183 2.485086901 -0.037928336
6 0.725787474 1.250353341 -0.001539732
6 0.739853552 -1.167748028 -0.020982015
6 2.142159249 -1.166479489 -0.026115009
6 2.150693385 1.241655457 0.012056303
6 2.145387402 3.671603031 -0.007541485
6 0.739696008 3.675868114 -0.039536914
7 -1.363420688 0.016179865 -0.062974898
1 3.940376021 0.028288071 0.006272796
1 3.926297501 2.464521877 0.018642964
1 -1.044818066 2.489473673 -0.107059570
1 0.187845382 -2.118852568 -0.024323365
1 2.674422682 -2.126356814 -0.043517514
1 2.694544726 4.624088114 -0.017596128
1 0.193117454 4.628430336 -0.084691499
1 -1.800003163 0.717067320 0.547694977
1 -1.769329947 -0.907255040 0.125147620
Read a general xyz format, putting the coordinates into apos, the char string names into atype, and the charges in charge.
Here is a sample file:
SILICON 14.0 2.9639742677 -2.9639742677 -2.9639742677 SILICON 14.0 -2.9639742677 2.9639742677 -2.9639742677 SILICON 14.0 -2.9639742677 -2.9639742677 2.9639742677 SILICON 14.0 -2.9639742677 2.9639742677 2.9639742677 SILICON 14.0 2.9639742677 2.9639742677 -2.9639742677 SILICON 14.0 -2.9639742677 -2.9639742677 -2.9639742677 SILICON 14.0 2.9639742677 -2.9639742677 2.9639742677 SILICON 14.0 2.9639742677 2.9639742677 2.9639742677 OXYGEN 8.0 .0000000000 -3.5306894327 -3.5306894327 OXYGEN 8.0 .0000000000 3.5306894327 -3.5306894327 OXYGEN 8.0 .0000000000 -3.5306894327 3.5306894327 OXYGEN 8.0 3.5306894327 .0000000000 3.5306894327 OXYGEN 8.0 -3.5306894327 .0000000000 -3.5306894327 OXYGEN 8.0 -3.5306894327 .0000000000 3.5306894327 OXYGEN 8.0 3.5306894327 .0000000000 -3.5306894327 OXYGEN 8.0 3.5306894327 3.5306894327 .0000000000 OXYGEN 8.0 -3.5306894327 -3.5306894327 .0000000000 OXYGEN 8.0 3.5306894327 -3.5306894327 .0000000000 OXYGEN 8.0 -3.5306894327 3.5306894327 .0000000000 OXYGEN 8.0 .0000000000 3.5306894327 3.5306894327 HYDROGEN 1.0 4.5627046338 -4.5627046338 -4.5627046338 HYDROGEN 1.0 -4.5627046338 4.5627046338 -4.5627046338 HYDROGEN 1.0 -4.5627046338 -4.5627046338 4.5627046338 HYDROGEN 1.0 -4.5627046338 4.5627046338 4.5627046338 HYDROGEN 1.0 4.5627046338 4.5627046338 -4.5627046338 HYDROGEN 1.0 -4.5627046338 -4.5627046338 -4.5627046338 HYDROGEN 1.0 4.5627046338 -4.5627046338 4.5627046338 HYDROGEN 1.0 4.5627046338 4.5627046338 4.5627046338
Read in GAMESS xyz format from the PERL extraction, putting the coordinates into apos, the char string names into atype, and the charges in charge.
Here is a sample file:
1 C 6.0 0.0000000000 0.0000000000 -0.1699098334 2 H 1.0 -1.6872904675 0.0000000000 1.0115436711 3 H 1.0 1.6872904675 0.0000000000 1.0115436711<H1 ALIGN="center"> <A NAME="esp">Mopac Electrostatic Potential</A> called <I>mopac esp</I></H1> <P> Read a CONVEX mopac ESP file, putting the coordinates into <B>apos</B> and the char string names into <B>atype</B>. Return number of atoms. Stop reading on End-of-file, or 'END' line, or line with just a ".". </P> <P> Here is a sample file: </P>protonated complex structure 1 backbone anchored PM3 XYZ MMOK SETUP=KEYS AVSWAVE 1SCF GNORM=0.001 SCFCRT=1.0D-10 NOLOG PRECISE NOANCI NODIIS 130 -23.124657 -22.388311 -21.155438 322 0.000000 0.000000 0.755905 -1 0.000000 0.755905 0.000000 322 0.755905 0.000000 0.000000 6 0.6000000E+01 -0.7892052E+01 -0.1296199E+02 0.2722263E+01 1 0.1000000E+01 -0.5812176E+01 -0.1296199E+02 0.2722263E+01 6 0.6000000E+01 -0.8921321E+01 -0.1031720E+02 0.2722263E+01CHEM3D called chem3d
Read a CHEM-3D file, putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop reading on End-of-file, or 'END' line, or line with just a ".".
Here is a sample file:
540 C 1 -6.345535 -0.819672 8.125168 1 2 6 111 C 2 -5.099655 -1.005203 8.798187 1 1 3 173 C 3 -4.514252 -2.309235 8.871323 1 2 4 216 C 4 -5.176743 -3.422500 8.273132 1 3 5 221 C 5 -6.482925 -3.259781 7.752930 1 4 6 7MOL called mol
Read a MOL file, putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop reading on End-of-file, or 'END' line, or line with just a ".".
Here is a sample file:
1.000 1.000 1.000 90.000 90.000 90.000 61 1 O -1.99050 -3.82015 -0.25595 21 41 0 0 0 0 2 O -3.53075 0.44747 0.16308 22 42 0 0 0 0 3 O 0.82619 -3.51817 0.62851 23 43 0 0 0 0 4 O -2.98560 1.99548 -2.14861 24 44 0 0 0 0 5 O -0.54806 2.46364 -0.81459 25 45 0 0 0 0 6 O 1.64986 3.31839 -2.11407 26 46 0 0 0 0MOL2 called mol2
Read a TRIPOS MOL2 file, putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop reading on End-of-file, or 'END' line, or line with just a ".".
Here is a sample file:
# Name: ACETYLCHOLINESTERASE-EDROPHONIUM COMPLEX (ACHE-EDR) # Creating user name: maria # Creation time: Wed Dec 1 12:50:27 1993 # Modifying user name: maria # Modification time: Wed Dec 1 12:50:27 1993 @<TRIPOS>MOLECULE ACETYLCHOLINESTERASE-EDROPHONIUM COMPLEX (ACHE-EDR) 7652 8211 529 0 9 PROTEIN NO_CHARGES @<TRIPOS>DICT PROTEIN PROTEIN @<TRIPOS>ATOM 1 N -12.6074 -23.1989 -24.7946 N.am 1 SER4 0.0000 BACKBONE|DICT|DIRECT 2 CA -11.6823 -23.4022 -25.9155 C.3 1 SER4 0.0000 BACKBONE|DICT|DIRECT 3 CB -12.3635 -23.2206 -27.2850 C.3 1 SER4 0.0000 DICT 4 OG -13.4899 -24.1115 -27.1791 O.3 1 SER4 0.0000 DICT 5 C -10.5679 -22.4829 -25.5506 C.2 1 SER4 0.0000 BACKBONE|DICT|DIRECT 6 O -10.8245 -21.7067 -24.6525 O.2 1 SER4 0.0000 BACKBONE|DICT|DIRECT 7 N -9.4054 -22.5321 -26.1952 N.am 2 GLU5 0.0000 BACKBONE|DICT|DIRECT 8 CA -8.3110 -21.6834 -25.7109 C.3 2 GLU5 0.0000 BACKBONE|DICT|DIRECT 9 CB -7.2229 -21.5776 -26.7863 C.3 2 GLU5 0.0000 DICT 10 CG -5.8910 -20.9530 -26.3251 C.3 2 GLU5 0.0000 DICT 11 CD -4.9174 -21.9241 -25.6819 C.2 2 GLU5 0.0000 DICT 12 OE1 -5.1290 -22.2838 -24.5283 O.co2 2 GLU5 0.0000 DICT @<TRIPOS>BOND 1 2 13 1 BACKBONE|DICT 2 2 3 1 DICT 3 2 1 1 BACKBONE|DICT @<TRIPOS>SUBSTRUCTURE 1 TRP84 2 RESIDUE 1 A TRP 0 ROOT 2 SER200 16 RESIDUE 1 A SER 0 ROOT 3 PHE330 22 RESIDUE 1 A PHE 0 ROOT 4 HIS440 33 RESIDUE 1 A HIS 0 ROOT 5 THA999 42 GROUP 0 A **** 0 ROOT @<TRIPOS>SET UNK_ATOMS STATIC ATOMS AMSOM **** 15 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 ATOM$BY_TYPE STATIC ATOMS COLORGROUP SYSTEM 15 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 ATOM$MAGENTA STATIC ATOMS COLORGROUP SYSTEM 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 \ 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 \ 38 39 40 41Molecular Mechanics Code MM3 called mm3
Read a MM3 coordinate file, putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop reading on End-of-file, or 'END' line, or line with just a ".".
Here is a sample file:
ETHANOL 0 9 0 0 0 0 10.0 0 1 0.0000000 6 0 0 0 0 0 1 1 0 1 2 3 1 4 1 5 1 6 2 7 2 8 3 9 1.27819 -0.24461 0.00000 C 1( 1) -0.01083 0.57083 0.00000 C 1( 2) -1.12978 -0.32457 0.00000 O 6( 3) 2.17404 0.41427 0.00000 H 5( 4) 1.34833 -0.89848 0.89680 H 5( 5) 1.34833 -0.89848 -0.89680 H 5( 6) -0.05313 1.22856 0.90370 H 5( 7) -0.05313 1.22856 -0.90370 H 5( 8) -1.92470 0.19229 0.00000 H 21( 9)Mopac coordinates called mopac xyz
Read a MOPAC xyz coordinate file, putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop reading on End-of-file, blank line or blank atom.
Here is a sample file:
AM1 XYZ T=02.00D GNORM=0.01 MODE=1 SCFCRT=1.D-7 LET /users/natalia/chris12.dat chris12 O 0.0000000000000 1 0.0000000000000 1 0.0000000000000 1 N 1.1593000000000 1 0.0000000000000 1 0.0000000000000 1 C 1.8677000000000 1 1.2712000000000 1 0.0000000000000 1 C 3.2845000000000 1 1.2280000000000 1 0.0040000000000 1Gaussian© Cube Files called Cube
Read a CUBE file from Gaussian, putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop after coordinate read.
Here is a sample file:
Gaussian Test Job 318: Potential cube SCF Total Density 3 -9.393328 -9.393328 -8.985941 10 2.087406 0.000000 0.000000 10 0.000000 2.087406 0.000000 10 0.000000 0.000000 2.087406 8 8.000000 0.000000 0.000000 0.215580 1 1.000000 0.000000 1.435626 -0.862319 1 1.000000 0.000000 -1.435626 -0.862319 1.88175E-03 1.79419E-03 1.51013E-03 9.93986E-04 2.86401E-04 -4.81750E-04 -1.14728E-03 -1.60245E-03 -1.83108E-03 -1.87998E-03GAMESS Plotting Option called CGamess
Read a CUBE like file from GAMESS, putting the coordinates into apos and the char string names into atype. Return number of atoms. Stop after coordinate read.
Here is a sample file:
#of_atoms #of_vectors #of_x_pts #of_y_pts #of_z_pts xmin xmax ymin ymax zmin zmax coordinates in GAMESS_format vec1 vec2 vec3 ... vec_max_numPlain Coordinates called PlainCoord
The PlainCoord option is to process a simple file of X-Y-Z coordinates with the atom type designated by the entry in the periodic table. This format is nearly identical to the DmolXYZ file format
Here is a sample file:
6 -1.415689945221 0.020083000883 0.255733013153 6 -0.670023024082 1.240668058395 -0.075638003647 6 0.656983017921 1.203186035156 -0.208253994584 6 1.393203973770 0.004366000183 0.352591007948 6 0.647606015205 -1.161679029465 -0.286873012781 6 -0.810204029083 -1.153972029686 0.065237000585 1 -1.350576043129 -2.081850051880 0.066707000136 1 -2.466548919678 0.082985997200 0.463546991348 1 -1.231073021889 2.113032102585 -0.355015993118 1 1.204282999039 2.023315906525 -0.632936000824 1 2.443694114685 0.003373000072 0.092260003090 1 1.132277011871 -2.126605033875 -0.221330001950 1 1.316627025604 -0.007073000073 1.437821984291 1 0.618321001530 -0.923030018806 -1.357839941978