Wed Dec 28 11:01:21 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 Wed Dec 28 2011 at 11:01:21 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6426457 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): -3.732000 35.22600 ymin,ymax (A): -4.584000 48.74300 zmin,zma (A): -24.06200 31.33400 x,y,z range (A): 38.95800 53.32700 55.39600 scale (grids/A): 0.6426457 object centre (A): 15.74700 22.07950 3.636000 number of atom coordinates read : 1963 total number of charged atoms : 1830 net assigned charge : 4.681007 assigned positive charge : 287.8141 centred at (gu) : 90.09147 92.91325 90.00991 assigned negative charge : -283.1333 centred at (gu) : 90.15028 93.01519 89.93803 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5665 nv = 96 ne = 84 npr = 40237 no. pairs analyzed = 40237 no. exposed pairs = 2356 no. arc points = 16989 no. surface atoms = 800 nbur = 1163 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 296 mr = 3244 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3000000 number of dielectric boundary points 2678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1679 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0414939E-09 1.4082088E-08 midg,1,midg; midg,igrid,midg 9.1091756E-09 -3.7904075E-09 1,midg,midg; igrid,midg,midg 1.2640117E-08 2.2800266E-09 gauss-seidel spectral radius is 0.9873990 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 11:01:22 rms-change max change #iterations 0.1222835 17.93545 at 10iterations 1.2197898E-02 1.911453 at 20iterations 1.2539732E-03 0.2400284 at 30iterations 1.2238242E-04 2.0286560E-02 at 40iterations 1.2249378E-05 1.7038584E-03 at 50iterations finished qdiffx linear iterations at : 11:01:26 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 1.2249378E-05 1.7038584E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 11:01:27 4.572u 0.512s 0:05.79 87.7% 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 Wed Dec 28 2011 at 11:01:27 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.927937 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): -3.732000 35.22600 ymin,ymax (A): -4.584000 48.74300 zmin,zma (A): -24.06200 31.33400 x,y,z range (A): 38.95800 53.32700 55.39600 scale (grids/A): 1.927937 object centre (A): 15.74700 22.07950 3.636000 number of atom coordinates read : 1963 total number of charged atoms : 1830 net assigned charge : 4.681007 assigned positive charge : 287.8141 centred at (gu) : 90.27445 98.73962 90.02956 assigned negative charge : -283.1333 centred at (gu) : 90.45124 99.04588 89.81425 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 60074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16989 grid for indexing accessible points = 1.400000 m= 23145 mr = 41908 m= 3589 mr = 18066 m= 156 mr = 2345 m= 8 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1830 time to turn everything in is 0.5800000 number of dielectric boundary points 24588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14412 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) : 0.6426457 object centre at (A) : 15.74700 22.07950 3.636000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9330134E-02 2.5911696E-02 midg,1,midg; midg,igrid,midg 3.5257302E-02 3.1611638E-03 1,midg,midg; igrid,midg,midg 5.4543563E-03 -1.5585507E-04 gauss-seidel spectral radius is 0.9985886 estimated iterations to convergence 211 setup time was (sec) 0.9600000 now iterating at: 11:01:28 rms-change max change #iterations 3.619447 172.5986 at 10iterations 1.678144 66.50574 at 20iterations 0.7783078 27.42435 at 30iterations 0.3602665 13.59961 at 40iterations 0.1658442 5.640123 at 50iterations 7.6542795E-02 2.512852 at 60iterations 3.5448946E-02 1.321413 at 70iterations 1.6426871E-02 0.5640764 at 80iterations 7.5710951E-03 0.2697258 at 90iterations 3.5140943E-03 0.1164436 at 100iterations 1.6220206E-03 6.1314821E-02 at 110iterations 7.5013662E-04 2.5831223E-02 at 120iterations finished qdiffx linear iterations at : 11:01:39 total time elapsed so far: 11.60000 # loops : 120 mean,max change (kT/e) : 7.5013662E-04 2.5831223E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 11:01:39 11.786u 0.520s 0:12.64 97.3% 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 Wed Dec 28 2011 at 11:01:39 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.891906 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): -3.732000 35.22600 ymin,ymax (A): -4.584000 48.74300 zmin,zma (A): -24.06200 31.33400 x,y,z range (A): 38.95800 53.32700 55.39600 scale (grids/A): 2.891906 object centre (A): 15.74700 22.07950 3.636000 number of atom coordinates read : 1963 total number of charged atoms : 1830 net assigned charge : 4.681007 assigned positive charge : 287.8141 centred at (gu) : 90.41172 103.1095 90.04447 assigned negative charge : -283.1333 centred at (gu) : 90.67690 103.5689 89.72140 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 138685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16989 grid for indexing accessible points = 1.400000 m= 73160 mr = 101066 m= 28118 mr = 61409 m= 6340 mr = 23702 m= 792 mr = 4934 m= 49 mr = 565 m= 0 mr = 20 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 6284 time to turn everything in is 1.440000 number of dielectric boundary points 55448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 14637 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) : 1.927937 object centre at (A) : 15.74700 22.07950 3.636000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.110941 0.1114085 midg,1,midg; midg,igrid,midg 0.3453679 -6.8069496E-03 1,midg,midg; igrid,midg,midg 2.9961532E-02 5.4990347E-03 gauss-seidel spectral radius is 0.9992330 estimated iterations to convergence 285 setup time was (sec) 1.860000 now iterating at: 11:01:42 rms-change max change #iterations 8.414210 378.3978 at 10iterations 4.818838 111.8333 at 20iterations 2.738179 61.66447 at 30iterations 1.548106 33.92969 at 40iterations 0.8811781 18.72576 at 50iterations 0.5004838 10.10846 at 60iterations 0.2839855 5.913477 at 70iterations 0.1610003 3.324829 at 80iterations 9.1455638E-02 1.759623 at 90iterations 5.1849682E-02 1.068600 at 100iterations 2.9406182E-02 0.6225204 at 110iterations 1.6658068E-02 0.3419952 at 120iterations 9.4423089E-03 0.1852417 at 130iterations 5.3628129E-03 0.1013947 at 140iterations 3.0447782E-03 6.3541412E-02 at 150iterations 1.7295417E-03 3.5224915E-02 at 160iterations 9.8022772E-04 1.8188477E-02 at 170iterations 5.5867934E-04 1.1634827E-02 at 180iterations finished qdiffx linear iterations at : 11:02:00 total time elapsed so far: 20.09000 # loops : 180 mean,max change (kT/e) : 5.5867934E-04 1.1634827E-02 energy calculations done at 20.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.26000 DelPhi exited at 11:02:02 20.265u 0.545s 0:22.60 92.0% 0+0k 0+0io 0pf+0w