Sat Oct 8 19:56:10 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 Sat Oct 8 2011 at 19:56:10 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 483 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6150762 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): -31.15800 17.54700 ymin,ymax (A): -23.33000 23.49400 zmin,zma (A): -12.63300 45.24600 x,y,z range (A): 48.70500 46.82400 57.87900 scale (grids/A): 0.6150762 object centre (A): -6.805499 8.1999779E-02 16.30650 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.40478 88.94824 89.70622 assigned negative charge : -387.4045 centred at (gu) : 88.30916 88.99599 89.57817 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6316 nv = 96 ne = 84 npr = 54521 no. pairs analyzed = 54521 no. exposed pairs = 3000 no. arc points = 21233 no. surface atoms = 1009 nbur = 1580 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 332 mr = 3556 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.1900000 number of dielectric boundary points 3064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2120 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7919 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9031681E-09 9.4379775E-09 midg,1,midg; midg,igrid,midg 7.0352062E-09 1.1306926E-10 1,midg,midg; igrid,midg,midg -3.9277706E-09 5.8195679E-09 gauss-seidel spectral radius is 0.9863061 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 19:56:10 rms-change max change #iterations 0.1214597 19.82303 at 10iterations 1.0715911E-02 1.714631 at 20iterations 1.0007478E-03 0.1434402 at 30iterations 9.0019945E-05 1.5121460E-02 at 40iterations 8.2268170E-06 1.2073517E-03 at 50iterations finished qdiffx linear iterations at : 19:56:13 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 8.2268170E-06 1.2073517E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 19:56:14 3.539u 0.194s 0:04.05 91.8% 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 19:56:14 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 483 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.845229 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): -31.15800 17.54700 ymin,ymax (A): -23.33000 23.49400 zmin,zma (A): -12.63300 45.24600 x,y,z range (A): 48.70500 46.82400 57.87900 scale (grids/A): 1.845229 object centre (A): -6.805499 8.1999779E-02 16.30650 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.21361 86.84443 89.11832 assigned negative charge : -387.4045 centred at (gu) : 84.92750 86.98744 88.73433 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 69097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21233 grid for indexing accessible points = 1.400000 m= 23351 mr = 48401 m= 3200 mr = 17151 m= 132 mr = 1989 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4070 time to turn everything in is 0.3700000 number of dielectric boundary points 28208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19273 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) : 0.6150762 object centre at (A) : -6.805499 8.1999779E-02 16.30650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5985195E-02 2.7535466E-02 midg,1,midg; midg,igrid,midg 1.2338856E-02 1.7946217E-03 1,midg,midg; igrid,midg,midg -2.5611703E-04 2.6904736E-02 gauss-seidel spectral radius is 0.9985405 estimated iterations to convergence 208 setup time was (sec) 0.6300000 now iterating at: 19:56:15 rms-change max change #iterations 3.941468 158.9697 at 10iterations 1.802080 62.55580 at 20iterations 0.8189259 28.77333 at 30iterations 0.3737859 12.44372 at 40iterations 0.1710242 5.947641 at 50iterations 7.8071050E-02 2.434613 at 60iterations 3.5586551E-02 1.369545 at 70iterations 1.6294234E-02 0.5603981 at 80iterations 7.4519706E-03 0.2769766 at 90iterations 3.4041379E-03 0.1171904 at 100iterations 1.5513328E-03 5.5016518E-02 at 110iterations 7.1143935E-04 2.7647018E-02 at 120iterations finished qdiffx linear iterations at : 19:56:23 total time elapsed so far: 8.970000 # loops : 120 mean,max change (kT/e) : 7.1143935E-04 2.7647018E-02 energy calculations done at 8.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.090000 DelPhi exited at 19:56:23 9.095u 0.275s 0:09.66 96.8% 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 19:56:23 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 483 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.767843 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): -31.15800 17.54700 ymin,ymax (A): -23.33000 23.49400 zmin,zma (A): -12.63300 45.24600 x,y,z range (A): 48.70500 46.82400 57.87900 scale (grids/A): 2.767843 object centre (A): -6.805499 8.1999779E-02 16.30650 number of atom coordinates read : 2589 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.82030 85.26640 88.67727 assigned negative charge : -387.4045 centred at (gu) : 82.39129 85.48118 88.10136 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 159950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21233 grid for indexing accessible points = 1.400000 m= 78023 mr = 117226 m= 25800 mr = 63887 m= 5564 mr = 20705 m= 616 mr = 4199 m= 26 mr = 386 m= 0 mr = 12 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 13899 time to turn everything in is 0.8900000 number of dielectric boundary points 63564 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19631 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) : 1.845229 object centre at (A) : -6.805499 8.1999779E-02 16.30650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6309415E-02 0.3419567 midg,1,midg; midg,igrid,midg 0.1342823 9.8080831E-03 1,midg,midg; igrid,midg,midg 7.2418172E-03 0.3620764 gauss-seidel spectral radius is 0.9992257 estimated iterations to convergence 284 setup time was (sec) 1.160000 now iterating at: 19:56:25 rms-change max change #iterations 9.301115 396.1069 at 10iterations 5.327376 132.9387 at 20iterations 3.021830 64.16527 at 30iterations 1.715988 33.51720 at 40iterations 0.9757867 18.12817 at 50iterations 0.5534644 11.39899 at 60iterations 0.3142936 6.243894 at 70iterations 0.1782586 3.864149 at 80iterations 0.1009357 1.763641 at 90iterations 5.7376038E-02 1.093907 at 100iterations 3.2504994E-02 0.6390004 at 110iterations 1.8445941E-02 0.3483238 at 120iterations 1.0450599E-02 0.2109680 at 130iterations 5.9210262E-03 0.1157341 at 140iterations 3.3643632E-03 6.7773819E-02 at 150iterations 1.9115767E-03 3.6012292E-02 at 160iterations 1.0871277E-03 2.0473003E-02 at 170iterations 6.1808911E-04 1.1653900E-02 at 180iterations finished qdiffx linear iterations at : 19:56:37 total time elapsed so far: 13.78000 # loops : 180 mean,max change (kT/e) : 6.1808911E-04 1.1653900E-02 energy calculations done at 13.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.91000 DelPhi exited at 19:56:38 13.909u 0.275s 0:14.49 97.7% 0+0k 0+0io 0pf+0w