Thu Jan 19 13:34:48 PST 2012 #!/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 Thu Jan 19 2012 at 13:34:50 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: 359 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6958 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4321437 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): -5.021000 77.35900 ymin,ymax (A): -0.7980000 73.96400 zmin,zma (A): 165.4150 235.2390 x,y,z range (A): 82.38000 74.76200 69.82401 scale (grids/A): 0.4321437 object centre (A): 36.16900 36.58300 200.3270 number of atom coordinates read : 6958 total number of charged atoms : 6789 net assigned charge : 5.200047 assigned positive charge : 1057.229 centred at (gu) : 89.22033 90.29492 89.70237 assigned negative charge : -1052.037 centred at (gu) : 89.18773 90.32005 89.66846 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7598 nv = 96 ne = 84 npr = 141213 no. pairs analyzed = 141213 no. exposed pairs = 9147 no. arc points = 61625 no. surface atoms = 3093 nbur = 3865 mkacc time = 0.2400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.932000 m= 206 mr = 3563 m= 0 mr = 1 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5107 ## 1072 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3742440E-12 3.3613765E-12 midg,1,midg; midg,igrid,midg 2.7870831E-12 -6.6639332E-13 1,midg,midg; igrid,midg,midg -1.4844945E-12 2.8259517E-12 gauss-seidel spectral radius is 0.9728342 estimated iterations to convergence 51 setup time was (sec) 0.6400000 now iterating at: 13:34:51 rms-change max change #iterations 3.2143287E-02 5.476639 at 10iterations 1.8868593E-03 0.3217869 at 20iterations 5.6649081E-04 8.6349487E-02 at 30iterations 2.0833811E-04 3.0675888E-02 at 40iterations 7.7389937E-05 1.0896683E-02 at 50iterations finished qdiffx linear iterations at : 13:34:59 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 7.7389937E-05 1.0896683E-02 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 13:35:00 3.825u 0.185s 0:10.50 38.0% 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 Thu Jan 19 2012 at 13:35:03 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: 359 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6958 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.296431 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): -5.021000 77.35900 ymin,ymax (A): -0.7980000 73.96400 zmin,zma (A): 165.4150 235.2390 x,y,z range (A): 82.38000 74.76200 69.82401 scale (grids/A): 1.296431 object centre (A): 36.16900 36.58300 200.3270 number of atom coordinates read : 6958 total number of charged atoms : 6789 net assigned charge : 5.200047 assigned positive charge : 1057.229 centred at (gu) : 87.65935 90.88316 89.10532 assigned negative charge : -1052.037 centred at (gu) : 87.56295 90.95982 89.00489 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 88472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61625 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 20768 mr = 57716 m= 1065 mr = 12187 m= 6 mr = 220 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 621 time to turn everything in is 0.4700000 number of dielectric boundary points 40188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1185 ## 43 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 47200 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) : 0.4321437 object centre at (A) : 36.16900 36.58300 200.3270 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5043448E-04 1.2353671E-04 midg,1,midg; midg,igrid,midg 6.3580158E-04 2.0262501E-03 1,midg,midg; igrid,midg,midg 2.4558380E-03 6.8688351E-03 gauss-seidel spectral radius is 0.9974490 estimated iterations to convergence 158 setup time was (sec) 0.7000000 now iterating at: 13:35:04 rms-change max change #iterations 3.138826 135.1899 at 10iterations 1.115971 40.35023 at 20iterations 0.3935522 14.67042 at 30iterations 0.1401476 4.872188 at 40iterations 4.9981587E-02 2.016857 at 50iterations 1.7795835E-02 0.6533947 at 60iterations 6.4815432E-03 0.2212944 at 70iterations 2.4830424E-03 0.1012840 at 80iterations 1.0938010E-03 4.6459198E-02 at 90iterations 5.9980055E-04 2.3805618E-02 at 100iterations 3.8886693E-04 1.4522552E-02 at 110iterations 2.6878022E-04 1.0197639E-02 at 120iterations finished qdiffx linear iterations at : 13:35:24 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 2.6878022E-04 1.0197639E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 13:35:25 8.100u 0.212s 0:22.30 37.2% 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 Thu Jan 19 2012 at 13:35:25 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: 359 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6958 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.944647 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): -5.021000 77.35900 ymin,ymax (A): -0.7980000 73.96400 zmin,zma (A): 165.4150 235.2390 x,y,z range (A): 82.38000 74.76200 69.82401 scale (grids/A): 1.944647 object centre (A): 36.16900 36.58300 200.3270 number of atom coordinates read : 6958 total number of charged atoms : 6789 net assigned charge : 5.200047 assigned positive charge : 1057.229 centred at (gu) : 86.48849 91.32418 88.65768 assigned negative charge : -1052.037 centred at (gu) : 86.34417 91.43966 88.50727 start vw surface at 0.1800000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 207322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61625 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 79931 mr = 144169 m= 14732 mr = 58522 m= 1075 mr = 9251 m= 25 mr = 398 m= 0 mr = 1 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1995 time to turn everything in is 1.110000 number of dielectric boundary points 90744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 53621 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) : 1.296431 object centre at (A) : 36.16900 36.58300 200.3270 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9980524E-02 -5.0571598E-03 midg,1,midg; midg,igrid,midg 2.0187363E-02 8.8541873E-02 1,midg,midg; igrid,midg,midg 0.2074744 0.2422097 gauss-seidel spectral radius is 0.9989981 estimated iterations to convergence 250 setup time was (sec) 1.390000 now iterating at: 13:35:27 rms-change max change #iterations 9.687889 276.8321 at 10iterations 5.314420 161.8022 at 20iterations 2.873657 81.55322 at 30iterations 1.546624 37.84005 at 40iterations 0.8253598 19.70030 at 50iterations 0.4413770 11.22766 at 60iterations 0.2343696 5.196001 at 70iterations 0.1240184 2.809510 at 80iterations 6.5644480E-02 1.445763 at 90iterations 3.4640618E-02 0.7326975 at 100iterations 1.8307842E-02 0.3960533 at 110iterations 9.6619846E-03 0.1844902 at 120iterations 5.0960290E-03 0.1143799 at 130iterations 2.6935490E-03 5.2316666E-02 at 140iterations 1.4340414E-03 3.1485319E-02 at 150iterations 7.7163201E-04 1.6342163E-02 at 160iterations 4.2690255E-04 1.0631084E-02 at 170iterations 2.4595889E-04 5.8975220E-03 at 180iterations finished qdiffx linear iterations at : 13:35:53 total time elapsed so far: 14.25000 # loops : 180 mean,max change (kT/e) : 2.4595889E-04 5.8975220E-03 energy calculations done at 14.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.39000 DelPhi exited at 13:35:54 14.390u 0.247s 0:28.72 50.9% 0+0k 0+0io 0pf+0w