* Test reading of MOL2 files by MMFF * external files: MMFFANG.PAR MMFFBOND.PAR MMFFCHG.PAR MMFFDEF.PAR * MMFFOOP.PAR MMFFSTBN.PAR MMFFSUP.PAR MMFFSYMB.PAR * MMFFTOR.PAR MMFFVDW.PAR * mmff_setup.STR * stream mmff_setup.str ! energies and GRMS for *.mrk files in the order ! used in this input file ! ! ENERgy GRMS mol or mrk file ! !ENER> 0 -52.58229 0.00000 7.05191 ! am07a !ENER> 0 39.32925 0.00000 0.03773 ! biphenyl.mrk !read individual structures, generate, write MERCK .mrk file, !perform minization and vibrational analysis set 1 am07a read mol2 unit 5 # Name: # Creating user name: ijen # Creation time: Thu May 27 13:29:06 1999 # Modifying user name: ijen # Modification time: Thu May 27 13:30:07 1999 @MOLECULE AM07A 8 7 1 0 0 PROTEIN GAST_HUCK @ATOM 1 O1 -0.1052 0.0000 0.1103 O.2 1 AAM07 -0.3715 2 C2 -0.0490 0.0000 1.3290 C.2 1 AAM07 0.1986 3 N3 1.1115 0.0000 2.0089 N.am 1 AAM07 -0.2032 4 C4 1.1030 0.0000 3.3538 C.2 1 AAM07 0.1986 5 O5 2.1220 0.0000 4.0248 O.2 1 AAM07 -0.3715 6 H6 -0.9661 0.0000 1.9164 H 1 AAM07 0.1610 7 H7 1.9892 0.0000 1.5296 H 1 AAM07 0.2270 8 H8 0.1296 0.0000 3.8421 H 1 AAM07 0.1610 @BOND 1 2 1 2 2 3 2 am 3 2 6 1 4 3 4 am 5 3 7 1 6 4 5 2 7 4 8 1 @SUBSTRUCTURE 1 AAM07 3 RESIDUE 1 A ALA 0 ROOT END goto mmfftst label am07a set 1 ar07a read mol2 unit 5 # Name: # Creating user name: ijen # Creation time: Thu May 27 14:01:00 1999 # Modifying user name: ijen # Modification time: Thu May 27 14:01:45 1999 @MOLECULE AR07A 9 9 1 0 0 PROTEIN GAST_HUCK @ATOM 1 O1 -0.3863 0.0000 0.3616 O.3 1 NFURA -0.2712 2 C2 -0.0617 0.0000 1.6874 C.2 1 NFURA 0.0766 3 C3 1.2931 0.0000 1.8468 C.2 1 NFURA -0.0687 4 C4 1.8496 0.0000 0.5328 C.2 1 NFURA -0.0687 5 C5 0.7912 0.0000 -0.3293 C.2 1 NFURA 0.0766 6 H6 -0.8482 0.0000 2.4406 H 1 NFURA 0.0951 7 H7 1.7237 0.0000 2.8471 H 1 NFURA 0.0327 8 H8 2.9303 0.0000 0.3991 H 1 NFURA 0.0327 9 H9 0.7836 0.0000 -1.4182 H 1 NFURA 0.0951 @BOND 1 1 2 1 2 5 1 1 3 3 2 2 4 2 6 1 5 4 3 1 6 3 7 1 7 5 4 2 8 4 8 1 9 5 9 1 @SUBSTRUCTURE 1 NFURA 5 RESIDUE 1 A ASN 0 ROOT END goto mmfftst label ar07a set 1 biphenyl read mol2 unit 5 # Name: # Creating user name: ijen # Creation time: Fri May 28 12:22:34 1999 # Modifying user name: ijen # Modification time: Fri May 28 12:23:25 1999 @MOLECULE BIPHENYL 22 23 1 0 0 PROTEIN GAST_HUCK @ATOM 1 C1 0.5604 1.3084 -0.0113 C.ar 1 BIPH1 -0.0617 2 C2 1.2482 0.2079 0.4912 C.ar 1 BIPH1 -0.0612 3 C3 0.6218 -1.0399 0.5554 C.ar 1 BIPH1 -0.0540 4 C4 -0.7030 -1.2084 0.1188 C.ar 1 BIPH1 -0.0179 5 C5 -1.3793 -0.0837 -0.3845 C.ar 1 BIPH1 -0.0540 6 C6 -0.7529 1.1641 -0.4496 C.ar 1 BIPH1 -0.0612 7 H7 1.0474 2.2756 -0.0608 H 1 BIPH1 0.0618 8 H8 2.2709 0.3180 0.8334 H 1 BIPH1 0.0618 9 H9 1.1588 -1.8964 0.9465 H 1 BIPH1 0.0624 10 H10 -2.4027 -0.1762 -0.7297 H 1 BIPH1 0.0624 11 H11 -1.2905 2.0198 -0.8418 H 1 BIPH1 0.0618 12 C12 -1.3445 -2.5398 0.1979 C.ar 1 BIPH1 -0.0179 13 C13 -2.5752 -2.6886 0.8599 C.ar 1 BIPH1 -0.0540 14 C14 -3.2001 -3.9358 0.9479 C.ar 1 BIPH1 -0.0612 15 C15 -2.6059 -5.0564 0.3740 C.ar 1 BIPH1 -0.0617 16 C16 -1.3858 -4.9309 -0.2868 C.ar 1 BIPH1 -0.0612 17 C17 -0.7619 -3.6837 -0.3738 C.ar 1 BIPH1 -0.0540 18 H18 -3.0547 -1.8282 1.3124 H 1 BIPH1 0.0624 19 H19 -4.1487 -4.0316 1.4635 H 1 BIPH1 0.0618 20 H20 -3.0924 -6.0227 0.4422 H 1 BIPH1 0.0618 21 H21 -0.9196 -5.8013 -0.7342 H 1 BIPH1 0.0618 22 H22 0.1868 -3.6070 -0.8927 H 1 BIPH1 0.0624 @BOND 1 2 1 ar 2 1 6 ar 3 1 7 1 4 2 3 ar 5 2 8 1 6 3 4 ar 7 3 9 1 8 4 5 ar 9 4 12 1 10 5 6 ar 11 5 10 1 12 6 11 1 13 12 13 ar 14 12 17 ar 15 13 14 ar 16 13 18 1 17 14 15 ar 18 14 19 1 19 15 16 ar 20 15 20 1 21 17 16 ar 22 16 21 1 23 17 22 1 @SUBSTRUCTURE 1 BIPH1 17 RESIDUE 1 A **** 0 ROOT END goto mmfftst label biphenyl stop label mmfftst !generate structure generate !write MERCK format file in output stream write merck unit 6 * test @1 * !create nobond list and calculate energy; note special terms required by MMFF ! update inbfrq -1 ihbfrq 0 CUTNB 999. CTOFNB 888. cdie e14fac 0.75 energy !energy minimization mini nrap nstep 20 nprint 1 vibran diag end goto @1