Tue Oct 11 05:59:54 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 Tue Oct 11 2011 at 05:59:54 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 = 2040 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: 0.7095875 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): 3.499000 47.23200 ymin,ymax (A): 0.8530000 40.01800 zmin,zma (A): -3.816000 46.35400 x,y,z range (A): 43.73300 39.16500 50.17000 scale (grids/A): 0.7095875 object centre (A): 25.36550 20.43550 21.26900 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 89.95123 90.83350 89.85041 assigned negative charge : -301.6792 centred at (gu) : 90.11801 90.81030 89.88524 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7055 nv = 96 ne = 84 npr = 40888 no. pairs analyzed = 40888 no. exposed pairs = 2463 no. arc points = 16862 no. surface atoms = 836 nbur = 1204 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 4085 m= 5 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1607 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7740 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6253841E-08 4.7590561E-08 midg,1,midg; midg,igrid,midg 4.6989985E-08 9.1436299E-08 1,midg,midg; igrid,midg,midg 1.5010562E-07 -1.8383584E-08 gauss-seidel spectral radius is 0.9896431 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 05:59:54 rms-change max change #iterations 0.2025095 26.19989 at 10iterations 2.5123825E-02 3.300729 at 20iterations 3.3565380E-03 0.4928055 at 30iterations 5.5683637E-04 6.8817854E-02 at 40iterations 1.3377264E-04 1.7808914E-02 at 50iterations finished qdiffx linear iterations at : 05:59:57 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.3377264E-04 1.7808914E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 05:59:57 3.442u 0.158s 0:03.90 92.0% 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 Tue Oct 11 2011 at 05:59:58 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 = 2040 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: 2.128762 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): 3.499000 47.23200 ymin,ymax (A): 0.8530000 40.01800 zmin,zma (A): -3.816000 46.35400 x,y,z range (A): 43.73300 39.16500 50.17000 scale (grids/A): 2.128762 object centre (A): 25.36550 20.43550 21.26900 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 89.85346 92.50028 89.55141 assigned negative charge : -301.6792 centred at (gu) : 90.35416 92.43098 89.65600 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 30727 mr = 53393 m= 6201 mr = 23541 m= 550 mr = 4173 m= 13 mr = 265 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 30905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15185 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) : 0.7095875 object centre at (A) : 25.36550 20.43550 21.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0692706E-02 5.4879360E-02 midg,1,midg; midg,igrid,midg 6.1495388E-03 3.2067046E-02 1,midg,midg; igrid,midg,midg 4.9733311E-02 1.5559771E-02 gauss-seidel spectral radius is 0.9988325 estimated iterations to convergence 232 setup time was (sec) 0.6100000 now iterating at: 05:59:58 rms-change max change #iterations 4.555404 242.0726 at 10iterations 2.259783 73.43259 at 20iterations 1.121429 38.55762 at 30iterations 0.5577356 20.01820 at 40iterations 0.2766888 8.750622 at 50iterations 0.1378883 4.663107 at 60iterations 6.8779632E-02 2.176389 at 70iterations 3.4221187E-02 1.071217 at 80iterations 1.7072886E-02 0.5320530 at 90iterations 8.5334135E-03 0.2570305 at 100iterations 4.2960751E-03 0.1339788 at 110iterations 2.1966856E-03 6.6368103E-02 at 120iterations finished qdiffx linear iterations at : 06:00:05 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.1966856E-03 6.6368103E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 06:00:06 7.904u 0.194s 0:08.55 94.6% 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 Tue Oct 11 2011 at 06:00:06 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 = 2040 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: 3.193143 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): 3.499000 47.23200 ymin,ymax (A): 0.8530000 40.01800 zmin,zma (A): -3.816000 46.35400 x,y,z range (A): 43.73300 39.16500 50.17000 scale (grids/A): 3.193143 object centre (A): 25.36550 20.43550 21.26900 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 89.78027 93.75041 89.32706 assigned negative charge : -301.6792 centred at (gu) : 90.53130 93.64641 89.48399 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 172162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 94961 mr = 128380 m= 39642 mr = 79414 m= 11799 mr = 32694 m= 2317 mr = 9209 m= 235 mr = 1675 m= 8 mr = 140 m= 0 mr = 4 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 69608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 15296 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) : 2.128762 object centre at (A) : 25.36550 20.43550 21.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2060262 0.5521036 midg,1,midg; midg,igrid,midg 3.0090975E-02 0.2349340 1,midg,midg; igrid,midg,midg 0.3934431 0.2453363 gauss-seidel spectral radius is 0.9992930 estimated iterations to convergence 297 setup time was (sec) 1.390000 now iterating at: 06:00:08 rms-change max change #iterations 10.14331 295.8574 at 10iterations 6.006325 153.8175 at 20iterations 3.553374 72.14053 at 30iterations 2.098047 39.91503 at 40iterations 1.233476 25.41165 at 50iterations 0.7242556 17.56777 at 60iterations 0.4253084 8.011875 at 70iterations 0.2496867 4.761692 at 80iterations 0.1460157 2.591468 at 90iterations 8.5663117E-02 1.782801 at 100iterations 5.0262664E-02 0.9067822 at 110iterations 2.9557075E-02 0.5861492 at 120iterations 1.7527143E-02 0.3200531 at 130iterations 1.0504524E-02 0.2051401 at 140iterations 6.4293388E-03 0.1272326 at 150iterations 4.0639821E-03 8.4255219E-02 at 160iterations 2.7054560E-03 5.1630020E-02 at 170iterations 1.9116350E-03 3.5743713E-02 at 180iterations finished qdiffx linear iterations at : 06:00:19 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 1.9116350E-03 3.5743713E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 06:00:20 12.768u 0.216s 0:13.75 94.3% 0+0k 0+0io 0pf+0w