Wed Dec 21 14:21:14 PST 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 Wed Dec 21 2011 at 14:21:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6546766 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): -4.611000 34.22200 ymin,ymax (A): -3.399000 48.25200 zmin,zma (A): -23.60400 30.77400 x,y,z range (A): 38.83300 51.65100 54.37800 scale (grids/A): 0.6546766 object centre (A): 14.80550 22.42650 3.585000 number of atom coordinates read : 1962 total number of charged atoms : 1828 net assigned charge : 3.362005 assigned positive charge : 293.1199 centred at (gu) : 90.42717 92.52844 90.08955 assigned negative charge : -289.7582 centred at (gu) : 90.55414 92.68394 90.01476 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5760 nv = 96 ne = 84 npr = 40432 no. pairs analyzed = 40432 no. exposed pairs = 2506 no. arc points = 17229 no. surface atoms = 854 nbur = 1108 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3191 m= 0 mr = 47 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.1700000 number of dielectric boundary points 2838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1708 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6660 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5812949E-09 1.7808031E-08 midg,1,midg; midg,igrid,midg 1.6298664E-08 -2.1512291E-08 1,midg,midg; igrid,midg,midg 2.1943588E-08 -9.2786676E-09 gauss-seidel spectral radius is 0.9878497 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 14:21:15 rms-change max change #iterations 0.1379170 24.98576 at 10iterations 1.4353993E-02 2.260115 at 20iterations 1.4971299E-03 0.2611237 at 30iterations 1.5407443E-04 2.8912067E-02 at 40iterations 1.5972979E-05 2.5537014E-03 at 50iterations finished qdiffx linear iterations at : 14:21:18 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.5972979E-05 2.5537014E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 14:21:28 3.970u 0.312s 0:14.38 29.7% 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 Wed Dec 21 2011 at 14:21:30 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.964030 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): -4.611000 34.22200 ymin,ymax (A): -3.399000 48.25200 zmin,zma (A): -23.60400 30.77400 x,y,z range (A): 38.83300 51.65100 54.37800 scale (grids/A): 1.964030 object centre (A): 14.80550 22.42650 3.585000 number of atom coordinates read : 1962 total number of charged atoms : 1828 net assigned charge : 3.362005 assigned positive charge : 293.1199 centred at (gu) : 91.28139 97.58548 90.26880 assigned negative charge : -289.7582 centred at (gu) : 91.66264 98.05217 90.04433 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 61408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17229 grid for indexing accessible points = 1.400000 m= 22717 mr = 42406 m= 3697 mr = 17195 m= 176 mr = 2386 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.3400000 number of dielectric boundary points 25961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14448 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) : 0.6546766 object centre at (A) : 14.80550 22.42650 3.585000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2161193E-02 1.5591346E-02 midg,1,midg; midg,igrid,midg 4.4659100E-02 -1.5315439E-02 1,midg,midg; igrid,midg,midg 1.0778035E-02 -5.5021103E-03 gauss-seidel spectral radius is 0.9986367 estimated iterations to convergence 215 setup time was (sec) 0.5600000 now iterating at: 14:21:32 rms-change max change #iterations 3.884634 172.0304 at 10iterations 1.823727 65.25747 at 20iterations 0.8555778 30.81541 at 30iterations 0.3984700 13.13565 at 40iterations 0.1877175 6.894271 at 50iterations 8.7938167E-02 2.979383 at 60iterations 4.1113161E-02 1.506582 at 70iterations 1.9241380E-02 0.6531982 at 80iterations 9.0212496E-03 0.2916358 at 90iterations 4.2066430E-03 0.1464591 at 100iterations 1.9792388E-03 6.6517591E-02 at 110iterations 9.2423963E-04 3.0792236E-02 at 120iterations finished qdiffx linear iterations at : 14:21:40 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 9.2423963E-04 3.0792236E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 14:21:49 8.446u 0.222s 0:18.44 46.9% 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 Wed Dec 21 2011 at 14:21:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.946044 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): -4.611000 34.22200 ymin,ymax (A): -3.399000 48.25200 zmin,zma (A): -23.60400 30.77400 x,y,z range (A): 38.83300 51.65100 54.37800 scale (grids/A): 2.946044 object centre (A): 14.80550 22.42650 3.585000 number of atom coordinates read : 1962 total number of charged atoms : 1828 net assigned charge : 3.362005 assigned positive charge : 293.1199 centred at (gu) : 91.92207 101.3782 90.40311 assigned negative charge : -289.7582 centred at (gu) : 92.49397 102.0784 90.06652 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 141606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17229 grid for indexing accessible points = 1.400000 m= 72639 mr = 102458 m= 27534 mr = 60062 m= 6733 mr = 22629 m= 911 mr = 5256 m= 40 mr = 583 m= 0 mr = 15 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 0.8400000 number of dielectric boundary points 58460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 14623 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) : 1.964030 object centre at (A) : 14.80550 22.42650 3.585000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9530017 4.5288619E-02 midg,1,midg; midg,igrid,midg 0.4635630 -0.2026981 1,midg,midg; igrid,midg,midg 7.7945717E-02 -2.7656615E-02 gauss-seidel spectral radius is 0.9992481 estimated iterations to convergence 288 setup time was (sec) 1.150000 now iterating at: 14:21:53 rms-change max change #iterations 9.049119 431.8684 at 10iterations 5.210115 126.4082 at 20iterations 2.990112 71.14623 at 30iterations 1.713459 35.44564 at 40iterations 0.9847150 21.64080 at 50iterations 0.5623592 12.48501 at 60iterations 0.3219256 6.207388 at 70iterations 0.1839397 3.479257 at 80iterations 0.1051462 2.179757 at 90iterations 6.0004670E-02 1.188992 at 100iterations 3.4345917E-02 0.6746502 at 110iterations 1.9582914E-02 0.3820114 at 120iterations 1.1198335E-02 0.2549400 at 130iterations 6.4043407E-03 0.1180611 at 140iterations 3.6516795E-03 7.1142197E-02 at 150iterations 2.0893370E-03 3.9087296E-02 at 160iterations 1.1918930E-03 2.2538185E-02 at 170iterations 6.8176951E-04 1.3698101E-02 at 180iterations finished qdiffx linear iterations at : 14:22:05 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 6.8176951E-04 1.3698101E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 14:22:11 13.208u 0.388s 0:21.16 64.1% 0+0k 0+0io 0pf+0w