Sat Oct 8 11:34:14 PDT 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+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 Sat Oct 8 2011 at 11:34:14 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 518 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6491375 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): -22.74600 32.09600 ymin,ymax (A): -1.782000 51.25800 zmin,zma (A): 11.51700 60.15800 x,y,z range (A): 54.84200 53.04000 48.64100 scale (grids/A): 0.6491375 object centre (A): 4.675000 24.73800 35.83750 number of atom coordinates read : 3363 total number of charged atoms : 3236 net assigned charge : -1.999971 assigned positive charge : 515.9114 centred at (gu) : 90.69460 90.75890 89.25092 assigned negative charge : -517.9123 centred at (gu) : 90.75517 90.56186 89.40773 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9372 nv = 96 ne = 84 npr = 70494 no. pairs analyzed = 70494 no. exposed pairs = 3651 no. arc points = 25128 no. surface atoms = 1241 nbur = 2122 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 524 mr = 5796 m= 2 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 153 time to turn everything in is 0.3500000 number of dielectric boundary points 4012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2390 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11309 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1153689E-08 -3.0597302E-08 midg,1,midg; midg,igrid,midg -3.7591533E-08 4.0292257E-08 1,midg,midg; igrid,midg,midg 6.6672663E-09 -1.8931628E-08 gauss-seidel spectral radius is 0.9877570 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 11:34:15 rms-change max change #iterations 0.1871787 23.86534 at 10iterations 1.9188583E-02 2.117706 at 20iterations 2.0286485E-03 0.2692299 at 30iterations 2.0885924E-04 2.9344082E-02 at 40iterations 2.1731348E-05 2.8009415E-03 at 50iterations finished qdiffx linear iterations at : 11:34:17 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 2.1731348E-05 2.8009415E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 11:34:18 3.165u 0.143s 0:03.66 90.1% 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 Sat Oct 8 2011 at 11:34:18 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 518 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.947412 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): -22.74600 32.09600 ymin,ymax (A): -1.782000 51.25800 zmin,zma (A): 11.51700 60.15800 x,y,z range (A): 54.84200 53.04000 48.64100 scale (grids/A): 1.947412 object centre (A): 4.675000 24.73800 35.83750 number of atom coordinates read : 3363 total number of charged atoms : 3236 net assigned charge : -1.999971 assigned positive charge : 515.9114 centred at (gu) : 92.08315 92.27566 87.75192 assigned negative charge : -517.9123 centred at (gu) : 92.26490 91.68512 88.22251 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 101009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25128 grid for indexing accessible points = 1.400000 m= 40015 mr = 74612 m= 6781 mr = 31747 m= 397 mr = 4721 m= 4 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 4439 time to turn everything in is 0.6600000 number of dielectric boundary points 36957 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 25501 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) : 0.6491375 object centre at (A) : 4.675000 24.73800 35.83750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9689692E-04 -6.6686504E-02 midg,1,midg; midg,igrid,midg -4.1472256E-02 4.4687800E-02 1,midg,midg; igrid,midg,midg 1.1217023E-04 -1.9210905E-02 gauss-seidel spectral radius is 0.9987460 estimated iterations to convergence 224 setup time was (sec) 0.9300000 now iterating at: 11:34:19 rms-change max change #iterations 5.240990 190.1399 at 10iterations 2.534492 74.19947 at 20iterations 1.225650 38.45741 at 30iterations 0.5944281 15.47429 at 40iterations 0.2879348 7.771122 at 50iterations 0.1394848 4.086941 at 60iterations 6.7368038E-02 1.725838 at 70iterations 3.2663655E-02 0.8525378 at 80iterations 1.5866006E-02 0.4504085 at 90iterations 7.6678903E-03 0.2065392 at 100iterations 3.7081386E-03 9.8547935E-02 at 110iterations 1.7974733E-03 4.9821854E-02 at 120iterations finished qdiffx linear iterations at : 11:34:25 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 1.7974733E-03 4.9821854E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 11:34:25 7.106u 0.168s 0:07.73 93.9% 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 Sat Oct 8 2011 at 11:34:26 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN5 518 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.921119 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): -22.74600 32.09600 ymin,ymax (A): -1.782000 51.25800 zmin,zma (A): 11.51700 60.15800 x,y,z range (A): 54.84200 53.04000 48.64100 scale (grids/A): 2.921119 object centre (A): 4.675000 24.73800 35.83750 number of atom coordinates read : 3363 total number of charged atoms : 3236 net assigned charge : -1.999971 assigned positive charge : 515.9114 centred at (gu) : 93.12447 93.41344 86.62761 assigned negative charge : -517.9123 centred at (gu) : 93.39726 92.52754 87.33361 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 233463 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25128 grid for indexing accessible points = 1.400000 m= 126998 mr = 178943 m= 50037 mr = 108510 m= 12514 mr = 42687 m= 1885 mr = 10119 m= 128 mr = 1306 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 14584 time to turn everything in is 1.710000 number of dielectric boundary points 83403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 25887 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) : 1.947412 object centre at (A) : 4.675000 24.73800 35.83750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5130024E-02 -0.7801187 midg,1,midg; midg,igrid,midg -0.4136361 0.4115663 1,midg,midg; igrid,midg,midg -0.1950019 -0.1883180 gauss-seidel spectral radius is 0.9992883 estimated iterations to convergence 296 setup time was (sec) 1.990000 now iterating at: 11:34:28 rms-change max change #iterations 11.93678 389.5671 at 10iterations 7.027659 127.4034 at 20iterations 4.119096 69.56542 at 30iterations 2.408854 43.14433 at 40iterations 1.409074 25.38683 at 50iterations 0.8200973 12.57707 at 60iterations 0.4786489 8.232971 at 70iterations 0.2785771 4.235443 at 80iterations 0.1620830 2.408482 at 90iterations 9.4210871E-02 1.602224 at 100iterations 5.4880131E-02 0.8021927 at 110iterations 3.1899169E-02 0.5686178 at 120iterations 1.8573761E-02 0.2877812 at 130iterations 1.0776210E-02 0.1657066 at 140iterations 6.2742680E-03 0.1026001 at 150iterations 3.6415667E-03 6.1952591E-02 at 160iterations 2.1191442E-03 3.2806873E-02 at 170iterations 1.2317017E-03 1.7717361E-02 at 180iterations finished qdiffx linear iterations at : 11:34:37 total time elapsed so far: 11.64000 # loops : 180 mean,max change (kT/e) : 1.2317017E-03 1.7717361E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 11:34:38 11.811u 0.184s 0:12.37 96.9% 0+0k 0+0io 0pf+0w