Sat Oct 15 13:05:48 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 15 2011 at 13:05:48 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3691 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.4962364 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): -19.45300 40.87400 ymin,ymax (A): -20.60400 34.30100 zmin,zma (A): -13.81700 57.92300 x,y,z range (A): 60.32700 54.90500 71.74000 scale (grids/A): 0.4962364 object centre (A): 10.71050 6.848501 22.05300 number of atom coordinates read : 3691 total number of charged atoms : 3541 net assigned charge : 5.500022 assigned positive charge : 570.4681 centred at (gu) : 89.43921 89.33507 90.73388 assigned negative charge : -564.9708 centred at (gu) : 89.35757 89.29977 90.69480 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5723 nv = 96 ne = 84 npr = 70584 no. pairs analyzed = 70584 no. exposed pairs = 4977 no. arc points = 35791 no. surface atoms = 1671 nbur = 2020 mkacc time = 0.1200000 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 = 1.708000 m= 186 mr = 2641 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3508 ## 664 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 7781 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3074364E-12 1.0150987E-10 midg,1,midg; midg,igrid,midg 2.2795110E-12 6.6262024E-11 1,midg,midg; igrid,midg,midg -5.7638248E-11 1.1076019E-10 gauss-seidel spectral radius is 0.9791711 estimated iterations to convergence 57 setup time was (sec) 0.4400000 now iterating at: 13:05:49 rms-change max change #iterations 5.0533123E-02 9.278091 at 10iterations 3.1388833E-03 0.5950012 at 20iterations 4.2337144E-04 0.1145134 at 30iterations 8.8130015E-05 2.3159027E-02 at 40iterations 1.9178935E-05 4.9362183E-03 at 50iterations finished qdiffx linear iterations at : 13:05:52 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.9178935E-05 4.9362183E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 13:05:52 3.561u 0.190s 0:04.03 93.0% 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 Sat Oct 15 2011 at 13:05:52 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3691 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.488709 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): -19.45300 40.87400 ymin,ymax (A): -20.60400 34.30100 zmin,zma (A): -13.81700 57.92300 x,y,z range (A): 60.32700 54.90500 71.74000 scale (grids/A): 1.488709 object centre (A): 10.71050 6.848501 22.05300 number of atom coordinates read : 3691 total number of charged atoms : 3541 net assigned charge : 5.500022 assigned positive charge : 570.4681 centred at (gu) : 88.31671 88.00399 92.20032 assigned negative charge : -564.9708 centred at (gu) : 88.07235 87.89907 92.08395 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 64600 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35791 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15874 mr = 40971 m= 1121 mr = 9528 m= 20 mr = 380 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 98 time to turn everything in is 0.3300000 number of dielectric boundary points 30736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 655 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 26292 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) : 0.4962364 object centre at (A) : 10.71050 6.848501 22.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7293178E-03 8.8470271E-03 midg,1,midg; midg,igrid,midg 2.3997098E-03 2.4544382E-03 1,midg,midg; igrid,midg,midg -2.9995756E-03 1.9182076E-03 gauss-seidel spectral radius is 0.9978740 estimated iterations to convergence 173 setup time was (sec) 0.5700000 now iterating at: 13:05:53 rms-change max change #iterations 3.074978 176.7549 at 10iterations 1.184263 48.34211 at 20iterations 0.4594271 18.95684 at 30iterations 0.1783982 6.850323 at 40iterations 6.9069542E-02 2.835819 at 50iterations 2.6950667E-02 0.9865990 at 60iterations 1.0587214E-02 0.3945069 at 70iterations 4.1745235E-03 0.1729622 at 80iterations 1.6891315E-03 6.7962646E-02 at 90iterations 7.1493501E-04 3.1845093E-02 at 100iterations 3.2062060E-04 1.5823364E-02 at 110iterations 1.5542847E-04 7.6656342E-03 at 120iterations finished qdiffx linear iterations at : 13:06:00 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.5542847E-04 7.6656342E-03 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 13:06:01 8.006u 0.198s 0:08.55 95.7% 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 Sat Oct 15 2011 at 13:06:01 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3691 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.233064 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): -19.45300 40.87400 ymin,ymax (A): -20.60400 34.30100 zmin,zma (A): -13.81700 57.92300 x,y,z range (A): 60.32700 54.90500 71.74000 scale (grids/A): 2.233064 object centre (A): 10.71050 6.848501 22.05300 number of atom coordinates read : 3691 total number of charged atoms : 3541 net assigned charge : 5.500022 assigned positive charge : 570.4681 centred at (gu) : 87.47456 87.00548 93.30033 assigned negative charge : -564.9708 centred at (gu) : 87.10846 86.84859 93.12583 start vw surface at 0.1100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150357 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35791 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 59310 mr = 101835 m= 12746 mr = 43623 m= 1515 mr = 8371 m= 58 mr = 787 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 308 time to turn everything in is 0.7500000 number of dielectric boundary points 69363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 28207 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) : 1.488709 object centre at (A) : 10.71050 6.848501 22.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5732139E-02 0.2477456 midg,1,midg; midg,igrid,midg 4.3549363E-02 3.4200590E-02 1,midg,midg; igrid,midg,midg -3.9863471E-02 1.5585843E-02 gauss-seidel spectral radius is 0.9990618 estimated iterations to convergence 258 setup time was (sec) 1.010000 now iterating at: 13:06:02 rms-change max change #iterations 8.697515 258.0053 at 10iterations 4.847976 141.6045 at 20iterations 2.685820 68.45205 at 30iterations 1.469396 38.26659 at 40iterations 0.8019620 19.61671 at 50iterations 0.4363522 11.43568 at 60iterations 0.2366044 5.580009 at 70iterations 0.1280548 2.881516 at 80iterations 6.9042854E-02 1.581299 at 90iterations 3.7306342E-02 0.8818893 at 100iterations 2.0073904E-02 0.4466705 at 110iterations 1.0803788E-02 0.2442939 at 120iterations 5.8233952E-03 0.1305618 at 130iterations 3.1524941E-03 7.5637817E-02 at 140iterations 1.7098648E-03 4.2218104E-02 at 150iterations 9.3128666E-04 2.2563934E-02 at 160iterations 5.1355059E-04 1.3542175E-02 at 170iterations 2.8923864E-04 7.9689026E-03 at 180iterations finished qdiffx linear iterations at : 13:06:14 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 2.8923864E-04 7.9689026E-03 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 13:06:14 12.849u 0.219s 0:13.41 97.3% 0+0k 0+0io 0pf+0w