Thu Jan 19 13:33:16 PST 2012 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Thu Jan 19 2012 at 13:33:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6758 !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4225369 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -61.88300 3.264000 ymin,ymax (A): -96.44100 -17.36500 zmin,zma (A): -27.98300 56.27000 x,y,z range (A): 65.14700 79.07600 84.25300 scale (grids/A): 0.4225369 object centre (A): -29.30950 -56.90300 14.14350 number of atom coordinates read : 6758 total number of charged atoms : 6588 net assigned charge : -6.942937 assigned positive charge : 1022.908 centred at (gu) : 91.08590 90.13725 88.53484 assigned negative charge : -1029.861 centred at (gu) : 91.09716 90.07908 88.47274 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7147 nv = 96 ne = 84 npr = 135885 no. pairs analyzed = 135885 no. exposed pairs = 8823 no. arc points = 60117 no. surface atoms = 2946 nbur = 3812 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.988000 m= 171 mr = 3342 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4879 ## 1066 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9905 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2554419E-12 9.9859086E-13 midg,1,midg; midg,igrid,midg -3.0055671E-12 1.5149291E-12 1,midg,midg; igrid,midg,midg -2.7745837E-13 -1.7810585E-12 gauss-seidel spectral radius is 0.9715928 estimated iterations to convergence 50 setup time was (sec) 0.6200000 now iterating at: 13:33:17 rms-change max change #iterations 2.9053988E-02 5.154095 at 10iterations 2.7481073E-03 0.4886284 at 20iterations 1.0369484E-03 0.1899166 at 30iterations 4.0829999E-04 7.4287415E-02 at 40iterations 1.6054192E-04 2.9109955E-02 at 50iterations finished qdiffx linear iterations at : 13:33:23 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 1.6054192E-04 2.9109955E-02 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 13:33:24 3.840u 0.189s 0:07.49 53.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Thu Jan 19 2012 at 13:33:24 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6758 !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.267611 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -61.88300 3.264000 ymin,ymax (A): -96.44100 -17.36500 zmin,zma (A): -27.98300 56.27000 x,y,z range (A): 65.14700 79.07600 84.25300 scale (grids/A): 1.267611 object centre (A): -29.30950 -56.90300 14.14350 number of atom coordinates read : 6758 total number of charged atoms : 6588 net assigned charge : -6.942937 assigned positive charge : 1022.908 centred at (gu) : 93.25512 90.40974 85.60210 assigned negative charge : -1029.861 centred at (gu) : 93.29133 90.23682 85.41743 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 84121 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60117 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 19334 mr = 55279 m= 956 mr = 11328 m= 6 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 493 time to turn everything in is 0.4600000 number of dielectric boundary points 37630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1145 ## 54 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 45362 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.4225369 object centre at (A) : -29.30950 -56.90300 14.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7000537E-02 1.0618319E-04 midg,1,midg; midg,igrid,midg -1.2843080E-03 4.8880785E-04 1,midg,midg; igrid,midg,midg 1.2984972E-03 -1.2888393E-03 gauss-seidel spectral radius is 0.9972978 estimated iterations to convergence 153 setup time was (sec) 0.7100000 now iterating at: 13:33:25 rms-change max change #iterations 2.916103 119.5002 at 10iterations 1.005767 43.95929 at 20iterations 0.3466231 13.36200 at 30iterations 0.1194849 4.051796 at 40iterations 4.1841742E-02 1.667479 at 50iterations 1.4798079E-02 0.5208817 at 60iterations 5.5963262E-03 0.2249737 at 70iterations 2.5375159E-03 0.1014290 at 80iterations 1.4687915E-03 5.9101105E-02 at 90iterations 9.8277710E-04 3.6302567E-02 at 100iterations 6.9187151E-04 2.5909424E-02 at 110iterations 4.9303577E-04 1.8192291E-02 at 120iterations finished qdiffx linear iterations at : 13:33:40 total time elapsed so far: 8.230000 # loops : 120 mean,max change (kT/e) : 4.9303577E-04 1.8192291E-02 energy calculations done at 8.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 13:33:41 8.369u 0.216s 0:16.72 51.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Thu Jan 19 2012 at 13:33:41 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6758 !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.901416 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -61.88300 3.264000 ymin,ymax (A): -96.44100 -17.36500 zmin,zma (A): -27.98300 56.27000 x,y,z range (A): 65.14700 79.07600 84.25300 scale (grids/A): 1.901416 object centre (A): -29.30950 -56.90300 14.14350 number of atom coordinates read : 6758 total number of charged atoms : 6588 net assigned charge : -6.942937 assigned positive charge : 1022.908 centred at (gu) : 94.88233 90.61381 83.40250 assigned negative charge : -1029.861 centred at (gu) : 94.93698 90.35506 83.12601 start vw surface at 0.1700000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 197366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60117 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 75689 mr = 138092 m= 13322 mr = 55512 m= 888 mr = 8237 m= 11 mr = 310 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1805 time to turn everything in is 1.030000 number of dielectric boundary points 85125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 51845 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.267611 object centre at (A) : -29.30950 -56.90300 14.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5223702 2.7797507E-02 midg,1,midg; midg,igrid,midg -2.5101122E-02 2.0044440E-02 1,midg,midg; igrid,midg,midg 3.1833459E-02 9.4408571E-04 gauss-seidel spectral radius is 0.9989443 estimated iterations to convergence 243 setup time was (sec) 1.290000 now iterating at: 13:33:42 rms-change max change #iterations 9.073362 282.9651 at 10iterations 4.858586 120.5170 at 20iterations 2.573963 64.42840 at 30iterations 1.357463 32.31717 at 40iterations 0.7133580 16.97265 at 50iterations 0.3728603 8.430763 at 60iterations 0.1947590 4.493173 at 70iterations 0.1011961 2.528982 at 80iterations 5.2686982E-02 1.288437 at 90iterations 2.7324947E-02 0.6157227 at 100iterations 1.4175929E-02 0.2922478 at 110iterations 7.3523470E-03 0.1732025 at 120iterations 3.8172370E-03 8.4266663E-02 at 130iterations 1.9848840E-03 4.0441990E-02 at 140iterations 1.0399400E-03 2.3736954E-02 at 150iterations 5.5293390E-04 1.1043549E-02 at 160iterations 3.0285245E-04 6.4907074E-03 at 170iterations 1.7511012E-04 4.6386719E-03 at 180iterations finished qdiffx linear iterations at : 13:34:05 total time elapsed so far: 13.60000 # loops : 180 mean,max change (kT/e) : 1.7511012E-04 4.6386719E-03 energy calculations done at 13.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.73000 DelPhi exited at 13:34:06 13.734u 0.233s 0:25.21 55.3% 0+0k 0+0io 0pf+0w