Tue Nov 22 14:16:48 PST 2011 #!/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+sph.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 = amb.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 Tue Nov 22 2011 at 14:16:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5877109 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): -35.25200 10.11200 ymin,ymax (A): 0.9350001 40.93000 zmin,zma (A): -2.182000 58.39200 x,y,z range (A): 45.36400 39.99500 60.57400 scale (grids/A): 0.5877109 object centre (A): -12.57000 20.93250 28.10500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.45802 89.72269 89.76488 assigned negative charge : -284.8263 centred at (gu) : 90.37424 89.83840 89.75248 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4532 nv = 96 ne = 84 npr = 40349 no. pairs analyzed = 40349 no. exposed pairs = 2392 no. arc points = 17059 no. surface atoms = 807 nbur = 1157 mkacc time = 7.0000000E-02 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 = 1.456000 m= 200 mr = 2482 m= 0 mr = 18 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1726 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4992156E-10 1.0124713E-09 midg,1,midg; midg,igrid,midg 3.1107439E-09 -1.2041651E-09 1,midg,midg; igrid,midg,midg -6.1917760E-10 2.6132116E-09 gauss-seidel spectral radius is 0.9849688 estimated iterations to convergence 67 setup time was (sec) 0.3600000 now iterating at: 14:16:56 rms-change max change #iterations 8.3238229E-02 14.94672 at 10iterations 6.8278252E-03 1.412109 at 20iterations 5.4253644E-04 9.5232010E-02 at 30iterations 4.2760341E-05 7.2979927E-03 at 40iterations 3.4053924E-06 6.4849854E-04 at 50iterations finished qdiffx linear iterations at : 14:17:05 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 3.4053924E-06 6.4849854E-04 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 14:17:07 3.640u 0.215s 0:15.02 25.6% 0+0k 0+0io 3pf+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 Tue Nov 22 2011 at 14:17:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.763133 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): -35.25200 10.11200 ymin,ymax (A): 0.9350001 40.93000 zmin,zma (A): -2.182000 58.39200 x,y,z range (A): 45.36400 39.99500 60.57400 scale (grids/A): 1.763133 object centre (A): -12.57000 20.93250 28.10500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.37408 89.16790 89.29472 assigned negative charge : -284.8263 centred at (gu) : 91.12305 89.51548 89.25774 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 49079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17059 grid for indexing accessible points = 1.400000 m= 17146 mr = 33511 m= 2268 mr = 12943 m= 93 mr = 1380 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 20727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14265 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) : 0.5877109 object centre at (A) : -12.57000 20.93250 28.10500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4047723E-02 1.8905809E-02 midg,1,midg; midg,igrid,midg 8.2967686E-04 -6.6382349E-03 1,midg,midg; igrid,midg,midg -8.0348877E-04 3.4884692E-05 gauss-seidel spectral radius is 0.9983314 estimated iterations to convergence 194 setup time was (sec) 0.5000000 now iterating at: 14:17:16 rms-change max change #iterations 3.073974 170.9850 at 10iterations 1.325249 56.08865 at 20iterations 0.5745566 24.49949 at 30iterations 0.2480615 9.950121 at 40iterations 0.1073942 4.469610 at 50iterations 4.6262607E-02 1.876972 at 60iterations 2.0125378E-02 0.8824530 at 70iterations 8.6816605E-03 0.3247337 at 80iterations 3.7426730E-03 0.1615868 at 90iterations 1.6238262E-03 6.4795494E-02 at 100iterations 7.0194551E-04 2.6539803E-02 at 110iterations 3.0295932E-04 1.2332916E-02 at 120iterations finished qdiffx linear iterations at : 14:17:39 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 3.0295932E-04 1.2332916E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 14:17:40 8.236u 0.240s 0:29.68 28.5% 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 Tue Nov 22 2011 at 14:17:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.644699 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): -35.25200 10.11200 ymin,ymax (A): 0.9350001 40.93000 zmin,zma (A): -2.182000 58.39200 x,y,z range (A): 45.36400 39.99500 60.57400 scale (grids/A): 2.644699 object centre (A): -12.57000 20.93250 28.10500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.06114 88.75172 88.94198 assigned negative charge : -284.8263 centred at (gu) : 91.68458 89.27332 88.88657 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 113501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17059 grid for indexing accessible points = 1.400000 m= 56577 mr = 81148 m= 19256 mr = 46828 m= 3802 mr = 15713 m= 408 mr = 2848 m= 11 mr = 279 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 46739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14651 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) : 1.763133 object centre at (A) : -12.57000 20.93250 28.10500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2554394 0.1133880 midg,1,midg; midg,igrid,midg -1.6269499E-02 -9.6528046E-02 1,midg,midg; igrid,midg,midg -2.8104825E-02 -4.0090859E-02 gauss-seidel spectral radius is 0.9991499 estimated iterations to convergence 271 setup time was (sec) 0.9200000 now iterating at: 14:17:48 rms-change max change #iterations 7.383493 237.2658 at 10iterations 4.070859 116.0796 at 20iterations 2.263570 54.21173 at 30iterations 1.243736 27.76610 at 40iterations 0.6855211 16.38246 at 50iterations 0.3763700 8.473129 at 60iterations 0.2071066 4.627373 at 70iterations 0.1137915 2.698812 at 80iterations 6.2759362E-02 1.567478 at 90iterations 3.4393679E-02 0.7730970 at 100iterations 1.8977145E-02 0.4062967 at 110iterations 1.0438732E-02 0.2368813 at 120iterations 5.7344958E-03 0.1342649 at 130iterations 3.1628828E-03 7.5305939E-02 at 140iterations 1.7361790E-03 3.8832664E-02 at 150iterations 9.5641328E-04 2.3588181E-02 at 160iterations 5.2782148E-04 1.2595654E-02 at 170iterations 2.9052046E-04 6.2718391E-03 at 180iterations finished qdiffx linear iterations at : 14:18:26 total time elapsed so far: 13.54000 # loops : 180 mean,max change (kT/e) : 2.9052046E-04 6.2718391E-03 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.66000 DelPhi exited at 14:18:28 13.665u 0.276s 0:45.93 30.3% 0+0k 0+0io 0pf+0w