Mon Oct 10 18:31:23 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 Mon Oct 10 2011 at 18:31:23 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2533 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 793 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5985910 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): -61.88000 -16.49700 ymin,ymax (A): -12.68500 44.86100 zmin,zma (A): -13.39700 46.07600 x,y,z range (A): 45.38300 57.54600 59.47300 scale (grids/A): 0.5985910 object centre (A): -39.18850 16.08800 16.33950 number of atom coordinates read : 2533 total number of charged atoms : 2394 net assigned charge : 15.60001 assigned positive charge : 381.9237 centred at (gu) : 89.81587 91.70560 89.09705 assigned negative charge : -366.3245 centred at (gu) : 89.89444 91.66221 89.13338 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6148 nv = 96 ne = 84 npr = 49946 no. pairs analyzed = 49946 no. exposed pairs = 3357 no. arc points = 24152 no. surface atoms = 1122 nbur = 1411 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 3138 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3500000 number of dielectric boundary points 3279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2472 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1754817E-09 4.2092370E-09 midg,1,midg; midg,igrid,midg 3.3870182E-09 1.1336506E-08 1,midg,midg; igrid,midg,midg 9.2438981E-09 3.5681413E-09 gauss-seidel spectral radius is 0.9855573 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 18:31:24 rms-change max change #iterations 0.1029335 17.42945 at 10iterations 8.6862268E-03 1.366074 at 20iterations 7.9736178E-04 0.1185150 at 30iterations 9.9267796E-05 1.8146515E-02 at 40iterations 1.7817898E-05 3.4189224E-03 at 50iterations finished qdiffx linear iterations at : 18:31:27 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.7817898E-05 3.4189224E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 18:31:28 4.140u 0.298s 0:04.95 89.4% 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 Mon Oct 10 2011 at 18:31:28 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2533 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 793 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.795773 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): -61.88000 -16.49700 ymin,ymax (A): -12.68500 44.86100 zmin,zma (A): -13.39700 46.07600 x,y,z range (A): 45.38300 57.54600 59.47300 scale (grids/A): 1.795773 object centre (A): -39.18850 16.08800 16.33950 number of atom coordinates read : 2533 total number of charged atoms : 2394 net assigned charge : 15.60001 assigned positive charge : 381.9237 centred at (gu) : 89.44701 95.11616 87.29042 assigned negative charge : -366.3245 centred at (gu) : 89.68306 94.98631 87.39989 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 66840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24152 grid for indexing accessible points = 1.400000 m= 21953 mr = 44579 m= 2779 mr = 15238 m= 145 mr = 1473 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1233 time to turn everything in is 0.6100000 number of dielectric boundary points 30404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 18705 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) : 0.5985910 object centre at (A) : -39.18850 16.08800 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1294714E-02 3.0575464E-02 midg,1,midg; midg,igrid,midg 1.7773479E-02 9.0169562E-03 1,midg,midg; igrid,midg,midg 2.5431834E-02 1.7018132E-02 gauss-seidel spectral radius is 0.9984637 estimated iterations to convergence 202 setup time was (sec) 0.9400000 now iterating at: 18:31:29 rms-change max change #iterations 3.683724 192.6554 at 10iterations 1.633998 65.95785 at 20iterations 0.7294905 27.10135 at 30iterations 0.3264721 10.82860 at 40iterations 0.1451914 4.861951 at 50iterations 6.4942203E-02 2.332823 at 60iterations 2.8901204E-02 0.9683390 at 70iterations 1.2961146E-02 0.4459505 at 80iterations 5.7768668E-03 0.2171559 at 90iterations 2.5882297E-03 9.0035915E-02 at 100iterations 1.1666456E-03 4.4528484E-02 at 110iterations 5.2256498E-04 1.7631531E-02 at 120iterations finished qdiffx linear iterations at : 18:31:38 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 5.2256498E-04 1.7631531E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 18:31:38 9.617u 0.287s 0:10.51 94.1% 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 Mon Oct 10 2011 at 18:31:39 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2533 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 793 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.693659 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): -61.88000 -16.49700 ymin,ymax (A): -12.68500 44.86100 zmin,zma (A): -13.39700 46.07600 x,y,z range (A): 45.38300 57.54600 59.47300 scale (grids/A): 2.693659 object centre (A): -39.18850 16.08800 16.33950 number of atom coordinates read : 2533 total number of charged atoms : 2394 net assigned charge : 15.60001 assigned positive charge : 381.9237 centred at (gu) : 89.17036 97.67426 85.93546 assigned negative charge : -366.3245 centred at (gu) : 89.52454 97.47929 86.09975 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 154805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24152 grid for indexing accessible points = 1.400000 m= 73411 mr = 108834 m= 23368 mr = 58334 m= 4690 mr = 17680 m= 539 mr = 3231 m= 21 mr = 257 m= 0 mr = 2 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 4111 time to turn everything in is 1.500000 number of dielectric boundary points 68496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19147 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) : 1.795773 object centre at (A) : -39.18850 16.08800 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6300127 0.3765413 midg,1,midg; midg,igrid,midg 0.3347753 0.1120085 1,midg,midg; igrid,midg,midg 0.2729232 0.1827381 gauss-seidel spectral radius is 0.9992167 estimated iterations to convergence 282 setup time was (sec) 1.830000 now iterating at: 18:31:41 rms-change max change #iterations 9.165628 277.8777 at 10iterations 5.335163 133.9863 at 20iterations 3.078893 72.84991 at 30iterations 1.763863 37.40092 at 40iterations 1.005053 23.78730 at 50iterations 0.5737807 12.31905 at 60iterations 0.3249865 7.067070 at 70iterations 0.1850108 3.900656 at 80iterations 0.1049845 1.934980 at 90iterations 5.9409138E-02 1.152696 at 100iterations 3.3748355E-02 0.6615486 at 110iterations 1.9052923E-02 0.3923149 at 120iterations 1.0784587E-02 0.2300038 at 130iterations 6.0916976E-03 0.1307144 at 140iterations 3.4512698E-03 7.3482513E-02 at 150iterations 1.9560040E-03 3.9251328E-02 at 160iterations 1.1091548E-03 2.3373604E-02 at 170iterations 6.3087733E-04 1.2218475E-02 at 180iterations finished qdiffx linear iterations at : 18:31:55 total time elapsed so far: 15.82000 # loops : 180 mean,max change (kT/e) : 6.3087733E-04 1.2218475E-02 energy calculations done at 15.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.01000 DelPhi exited at 18:31:55 16.008u 0.329s 0:16.64 98.0% 0+0k 0+0io 0pf+0w