Sat Oct 8 17:27:28 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 Sat Oct 8 2011 at 17:27:28 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 = 3545 !!! WARNING: ASL 224 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5126507 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): -5.639000 63.80400 ymin,ymax (A): 14.24400 76.50300 zmin,zma (A): -13.19200 34.38900 x,y,z range (A): 69.44300 62.25900 47.58100 scale (grids/A): 0.5126507 object centre (A): 29.08250 45.37350 10.59850 number of atom coordinates read : 3545 total number of charged atoms : 3398 net assigned charge : -7.099985 assigned positive charge : 540.9243 centred at (gu) : 90.08125 87.64427 89.44005 assigned negative charge : -548.0259 centred at (gu) : 90.08737 87.70468 89.45895 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5855 nv = 96 ne = 84 npr = 72195 no. pairs analyzed = 72195 no. exposed pairs = 4394 no. arc points = 30242 no. surface atoms = 1471 nbur = 2074 mkacc time = 0.1800000 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 = 1.652000 m= 214 mr = 3078 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 2984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2976 ## 472 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.3466435E-11 -1.3340842E-10 midg,1,midg; midg,igrid,midg 3.6029037E-11 -1.3325084E-10 1,midg,midg; igrid,midg,midg -9.8004084E-11 -1.2910434E-10 gauss-seidel spectral radius is 0.9804476 estimated iterations to convergence 59 setup time was (sec) 0.6800000 now iterating at: 17:27:29 rms-change max change #iterations 6.1467987E-02 11.15614 at 10iterations 3.4558224E-03 0.5552483 at 20iterations 2.0222868E-04 3.5966873E-02 at 30iterations 1.8596624E-05 3.0231476E-03 at 40iterations 3.5547903E-06 6.5708160E-04 at 50iterations finished qdiffx linear iterations at : 17:27:32 total time elapsed so far: 4.440000 # loops : 50 mean,max change (kT/e) : 3.5547903E-06 6.5708160E-04 energy calculations done at 4.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 17:27:33 4.610u 0.399s 0:05.32 93.9% 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 Sat Oct 8 2011 at 17:27:33 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 = 3545 !!! WARNING: ASL 224 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.537952 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): -5.639000 63.80400 ymin,ymax (A): 14.24400 76.50300 zmin,zma (A): -13.19200 34.38900 x,y,z range (A): 69.44300 62.25900 47.58100 scale (grids/A): 1.537952 object centre (A): 29.08250 45.37350 10.59850 number of atom coordinates read : 3545 total number of charged atoms : 3398 net assigned charge : -7.099985 assigned positive charge : 540.9243 centred at (gu) : 90.24279 82.93193 88.31897 assigned negative charge : -548.0259 centred at (gu) : 90.26176 83.11353 88.37650 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30242 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19427 mr = 45474 m= 1685 mr = 13152 m= 30 mr = 711 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.5500000 number of dielectric boundary points 27951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 427 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 25602 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) : 0.5126507 object centre at (A) : 29.08250 45.37350 10.59850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7425349E-03 -1.1364720E-03 midg,1,midg; midg,igrid,midg -1.2680561E-02 -1.2791843E-02 1,midg,midg; igrid,midg,midg 8.4127486E-03 -4.1570310E-03 gauss-seidel spectral radius is 0.9979889 estimated iterations to convergence 177 setup time was (sec) 0.8400000 now iterating at: 17:27:34 rms-change max change #iterations 3.268163 141.0480 at 10iterations 1.297522 46.96848 at 20iterations 0.5171123 19.01709 at 30iterations 0.2064987 8.443962 at 40iterations 8.2663745E-02 2.962247 at 50iterations 3.2867152E-02 1.213175 at 60iterations 1.3124079E-02 0.4468460 at 70iterations 5.2677779E-03 0.2036057 at 80iterations 2.0943112E-03 7.7385902E-02 at 90iterations 8.4120344E-04 2.8264999E-02 at 100iterations 3.3844836E-04 1.2058258E-02 at 110iterations 1.3770649E-04 5.2003860E-03 at 120iterations finished qdiffx linear iterations at : 17:27:44 total time elapsed so far: 10.33000 # loops : 120 mean,max change (kT/e) : 1.3770649E-04 5.2003860E-03 energy calculations done at 10.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 17:27:44 10.501u 0.450s 0:11.22 97.5% 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 17:27:44 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 = 3545 !!! WARNING: ASL 224 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.306928 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): -5.639000 63.80400 ymin,ymax (A): 14.24400 76.50300 zmin,zma (A): -13.19200 34.38900 x,y,z range (A): 69.44300 62.25900 47.58100 scale (grids/A): 2.306928 object centre (A): 29.08250 45.37350 10.59850 number of atom coordinates read : 3545 total number of charged atoms : 3398 net assigned charge : -7.099985 assigned positive charge : 540.9243 centred at (gu) : 90.36395 79.39771 87.47825 assigned negative charge : -548.0259 centred at (gu) : 90.39265 79.67001 87.56463 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 154049 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30242 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 69391 mr = 111398 m= 17775 mr = 54677 m= 2470 mr = 12945 m= 101 mr = 1543 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 525 time to turn everything in is 1.330000 number of dielectric boundary points 63206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 27117 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) : 1.537952 object centre at (A) : 29.08250 45.37350 10.59850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0005165E-03 -7.4538137E-03 midg,1,midg; midg,igrid,midg -0.2831458 -0.2618440 1,midg,midg; igrid,midg,midg 0.4265716 -8.0821127E-02 gauss-seidel spectral radius is 0.9990810 estimated iterations to convergence 261 setup time was (sec) 1.680000 now iterating at: 17:27:46 rms-change max change #iterations 8.737942 368.4976 at 10iterations 4.813096 127.7380 at 20iterations 2.635061 60.51793 at 30iterations 1.434045 34.74953 at 40iterations 0.7802199 17.81845 at 50iterations 0.4228232 9.752665 at 60iterations 0.2285219 4.615544 at 70iterations 0.1234905 2.666154 at 80iterations 6.6891544E-02 1.444999 at 90iterations 3.6164049E-02 0.7649721 at 100iterations 1.9508049E-02 0.4242721 at 110iterations 1.0518936E-02 0.2167282 at 120iterations 5.6614275E-03 0.1228101 at 130iterations 3.0619265E-03 6.6026688E-02 at 140iterations 1.6520380E-03 3.3859253E-02 at 150iterations 8.9180435E-04 1.7713070E-02 at 160iterations 4.8200195E-04 9.3975067E-03 at 170iterations 2.6179772E-04 5.4054260E-03 at 180iterations finished qdiffx linear iterations at : 17:28:02 total time elapsed so far: 17.42000 # loops : 180 mean,max change (kT/e) : 2.6179772E-04 5.4054260E-03 energy calculations done at 17.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.58000 DelPhi exited at 17:28:03 17.588u 0.462s 0:18.32 98.4% 0+0k 0+0io 0pf+0w