Sun Oct 9 05:17:05 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+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 Sun Oct 9 2011 at 05:17:05 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 = 2650 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6231511 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): -49.33900 2.800000 ymin,ymax (A): -25.88200 31.24700 zmin,zma (A): -37.04800 15.46600 x,y,z range (A): 52.13900 57.12900 52.51400 scale (grids/A): 0.6231511 object centre (A): -23.26950 2.682500 -10.79100 number of atom coordinates read : 2650 total number of charged atoms : 2512 net assigned charge : 2.500008 assigned positive charge : 389.1595 centred at (gu) : 90.58981 91.97111 91.64295 assigned negative charge : -386.6605 centred at (gu) : 90.64985 91.85365 91.67738 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7041 nv = 96 ne = 84 npr = 52761 no. pairs analyzed = 52761 no. exposed pairs = 3629 no. arc points = 25488 no. surface atoms = 1214 nbur = 1436 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3637 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2451 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8421 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2001191E-09 -6.3637406E-10 midg,1,midg; midg,igrid,midg -4.1559125E-09 1.6220445E-08 1,midg,midg; igrid,midg,midg 5.6128417E-09 -2.5971505E-09 gauss-seidel spectral radius is 0.9866782 estimated iterations to convergence 71 setup time was (sec) 0.6400000 now iterating at: 05:17:06 rms-change max change #iterations 0.1283424 22.67348 at 10iterations 1.1972080E-02 2.136814 at 20iterations 1.1386054E-03 0.1818056 at 30iterations 1.2642411E-04 1.8161774E-02 at 40iterations 2.3947006E-05 4.4860840E-03 at 50iterations finished qdiffx linear iterations at : 05:17:09 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 2.3947006E-05 4.4860840E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 05:17:10 4.079u 0.252s 0:04.67 92.5% 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 Sun Oct 9 2011 at 05:17:10 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 = 2650 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.869453 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): -49.33900 2.800000 ymin,ymax (A): -25.88200 31.24700 zmin,zma (A): -37.04800 15.46600 x,y,z range (A): 52.13900 57.12900 52.51400 scale (grids/A): 1.869453 object centre (A): -23.26950 2.682500 -10.79100 number of atom coordinates read : 2650 total number of charged atoms : 2512 net assigned charge : 2.500008 assigned positive charge : 389.1595 centred at (gu) : 91.76877 95.91285 94.92809 assigned negative charge : -386.6605 centred at (gu) : 91.94926 95.56057 95.03190 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25488 grid for indexing accessible points = 1.400000 m= 26336 mr = 50887 m= 4102 mr = 18756 m= 243 mr = 2401 m= 0 mr = 45 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 522 time to turn everything in is 0.6900000 number of dielectric boundary points 34693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 19706 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) : 0.6231511 object centre at (A) : -23.26950 2.682500 -10.79100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2410044E-02 3.7020317E-03 midg,1,midg; midg,igrid,midg -5.2911989E-02 3.1449557E-03 1,midg,midg; igrid,midg,midg 1.8770030E-02 2.0665613E-03 gauss-seidel spectral radius is 0.9985996 estimated iterations to convergence 212 setup time was (sec) 0.9800000 now iterating at: 05:17:11 rms-change max change #iterations 4.114748 161.5399 at 10iterations 1.900611 62.42737 at 20iterations 0.8787766 30.08001 at 30iterations 0.4074353 14.35885 at 40iterations 0.1887802 6.262120 at 50iterations 8.7411247E-02 2.824600 at 60iterations 4.0619411E-02 1.256844 at 70iterations 1.8816564E-02 0.6000550 at 80iterations 8.7114349E-03 0.2737331 at 90iterations 4.0516364E-03 0.1589887 at 100iterations 1.8908342E-03 6.1178446E-02 at 110iterations 8.8692538E-04 3.0775070E-02 at 120iterations finished qdiffx linear iterations at : 05:17:19 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 8.8692538E-04 3.0775070E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 05:17:20 9.453u 0.298s 0:10.08 96.6% 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 Sun Oct 9 2011 at 05:17:20 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 = 2650 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.804180 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): -49.33900 2.800000 ymin,ymax (A): -25.88200 31.24700 zmin,zma (A): -37.04800 15.46600 x,y,z range (A): 52.13900 57.12900 52.51400 scale (grids/A): 2.804180 object centre (A): -23.26950 2.682500 -10.79100 number of atom coordinates read : 2650 total number of charged atoms : 2512 net assigned charge : 2.500008 assigned positive charge : 389.1595 centred at (gu) : 92.65295 98.86911 97.39202 assigned negative charge : -386.6605 centred at (gu) : 92.92382 98.34078 97.54789 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 176245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25488 grid for indexing accessible points = 1.400000 m= 85730 mr = 124246 m= 30196 mr = 68530 m= 7223 mr = 23533 m= 966 mr = 5137 m= 53 mr = 574 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1834 time to turn everything in is 1.740000 number of dielectric boundary points 78386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 20096 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) : 1.869453 object centre at (A) : -23.26950 2.682500 -10.79100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1029290 2.3511155E-02 midg,1,midg; midg,igrid,midg -0.8724165 -0.1138709 1,midg,midg; igrid,midg,midg 0.2211896 -2.0840222E-02 gauss-seidel spectral radius is 0.9992606 estimated iterations to convergence 290 setup time was (sec) 2.080000 now iterating at: 05:17:22 rms-change max change #iterations 9.754830 350.9879 at 10iterations 5.765621 143.2135 at 20iterations 3.378822 79.72017 at 30iterations 1.972066 42.22022 at 40iterations 1.144060 25.30350 at 50iterations 0.6629809 13.60888 at 60iterations 0.3837444 7.685477 at 70iterations 0.2220555 4.437443 at 80iterations 0.1280705 2.528630 at 90iterations 7.3881008E-02 1.383547 at 100iterations 4.2564809E-02 0.8439894 at 110iterations 2.4538497E-02 0.4563599 at 120iterations 1.4126850E-02 0.2602863 at 130iterations 8.1304237E-03 0.1597725 at 140iterations 4.6965522E-03 8.4922731E-02 at 150iterations 2.7046762E-03 5.1392317E-02 at 160iterations 1.5662285E-03 2.8692245E-02 at 170iterations 9.1300858E-04 1.9114971E-02 at 180iterations finished qdiffx linear iterations at : 05:17:36 total time elapsed so far: 15.85000 # loops : 180 mean,max change (kT/e) : 9.1300858E-04 1.9114971E-02 energy calculations done at 15.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 05:17:37 16.030u 0.284s 0:16.58 98.3% 0+0k 0+0io 0pf+0w