Tue Oct 11 08:37:01 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 Tue Oct 11 2011 at 08:37:01 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7062652 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): 18.42300 64.24900 ymin,ymax (A): -3.661000 33.42700 zmin,zma (A): 19.75900 70.16500 x,y,z range (A): 45.82600 37.08800 50.40600 scale (grids/A): 0.7062652 object centre (A): 41.33600 14.88300 44.96200 number of atom coordinates read : 2109 total number of charged atoms : 1977 net assigned charge : 5.564012 assigned positive charge : 324.2660 centred at (gu) : 89.89337 89.62700 89.40591 assigned negative charge : -318.7021 centred at (gu) : 90.05152 89.66828 89.33685 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6978 nv = 96 ne = 84 npr = 42999 no. pairs analyzed = 42999 no. exposed pairs = 2520 no. arc points = 17081 no. surface atoms = 860 nbur = 1249 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 3975 m= 5 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1627 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2665065E-08 7.0937176E-08 midg,1,midg; midg,igrid,midg 7.0917551E-08 2.3754318E-08 1,midg,midg; igrid,midg,midg 1.2495431E-07 -3.2511412E-08 gauss-seidel spectral radius is 0.9895495 estimated iterations to convergence 80 setup time was (sec) 0.4600000 now iterating at: 08:37:02 rms-change max change #iterations 0.2068107 29.23491 at 10iterations 2.5705693E-02 3.791378 at 20iterations 3.3848684E-03 0.4433594 at 30iterations 5.2389468E-04 7.1074486E-02 at 40iterations 1.1711945E-04 1.6667366E-02 at 50iterations finished qdiffx linear iterations at : 08:37:04 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 1.1711945E-04 1.6667366E-02 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 08:37:05 3.032u 0.169s 0:03.67 86.9% 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 Tue Oct 11 2011 at 08:37:05 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.118795 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): 18.42300 64.24900 ymin,ymax (A): -3.661000 33.42700 zmin,zma (A): 19.75900 70.16500 x,y,z range (A): 45.82600 37.08800 50.40600 scale (grids/A): 2.118795 object centre (A): 41.33600 14.88300 44.96200 number of atom coordinates read : 2109 total number of charged atoms : 1977 net assigned charge : 5.564012 assigned positive charge : 324.2660 centred at (gu) : 89.67979 88.88107 88.21768 assigned negative charge : -318.7021 centred at (gu) : 90.15451 89.00490 88.01038 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17081 grid for indexing accessible points = 1.400000 m= 29427 mr = 52913 m= 5763 mr = 22313 m= 518 mr = 3928 m= 10 mr = 293 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 30754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15700 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) : 0.7062652 object centre at (A) : 41.33600 14.88300 44.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5217598E-02 5.4526143E-02 midg,1,midg; midg,igrid,midg 3.3730928E-02 2.5028582E-03 1,midg,midg; igrid,midg,midg 3.6496684E-02 2.1143029E-03 gauss-seidel spectral radius is 0.9988266 estimated iterations to convergence 231 setup time was (sec) 0.7900000 now iterating at: 08:37:06 rms-change max change #iterations 4.721699 202.4558 at 10iterations 2.341022 80.52081 at 20iterations 1.158108 36.35528 at 30iterations 0.5745617 17.56366 at 40iterations 0.2856995 9.190412 at 50iterations 0.1414617 4.063920 at 60iterations 7.0058405E-02 2.158032 at 70iterations 3.4938201E-02 1.035168 at 80iterations 1.7386511E-02 0.5210552 at 90iterations 8.7164314E-03 0.2803259 at 100iterations 4.3406086E-03 0.1308441 at 110iterations 2.2132818E-03 6.7047119E-02 at 120iterations finished qdiffx linear iterations at : 08:37:12 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 2.2132818E-03 6.7047119E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 08:37:12 6.948u 0.171s 0:07.60 93.5% 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 Tue Oct 11 2011 at 08:37:12 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.178193 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): 18.42300 64.24900 ymin,ymax (A): -3.661000 33.42700 zmin,zma (A): 19.75900 70.16500 x,y,z range (A): 45.82600 37.08800 50.40600 scale (grids/A): 3.178193 object centre (A): 41.33600 14.88300 44.96200 number of atom coordinates read : 2109 total number of charged atoms : 1977 net assigned charge : 5.564012 assigned positive charge : 324.2660 centred at (gu) : 89.51966 88.32160 87.32658 assigned negative charge : -318.7021 centred at (gu) : 90.23184 88.50732 87.01565 start vw surface at 0.1200000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 171699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17081 grid for indexing accessible points = 1.400000 m= 92397 mr = 127513 m= 37364 mr = 76940 m= 11044 mr = 30794 m= 2295 mr = 8642 m= 270 mr = 1751 m= 9 mr = 189 m= 0 mr = 6 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 69243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 15816 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) : 2.118795 object centre at (A) : 41.33600 14.88300 44.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1099580 0.4265851 midg,1,midg; midg,igrid,midg 0.3025658 -9.1187814E-03 1,midg,midg; igrid,midg,midg 0.3099823 0.1573040 gauss-seidel spectral radius is 0.9992958 estimated iterations to convergence 297 setup time was (sec) 1.940000 now iterating at: 08:37:14 rms-change max change #iterations 10.48182 404.6443 at 10iterations 6.189150 133.1682 at 20iterations 3.640862 76.76318 at 30iterations 2.147602 43.34695 at 40iterations 1.261104 21.76775 at 50iterations 0.7397585 14.40153 at 60iterations 0.4343567 7.774632 at 70iterations 0.2544098 4.555286 at 80iterations 0.1488227 2.596727 at 90iterations 8.7047234E-02 1.700986 at 100iterations 5.1109608E-02 0.9304428 at 110iterations 3.0062800E-02 0.5323639 at 120iterations 1.7739780E-02 0.3059616 at 130iterations 1.0587618E-02 0.1941662 at 140iterations 6.4448845E-03 0.1217651 at 150iterations 4.0058359E-03 7.2294235E-02 at 160iterations 2.6081258E-03 5.2059174E-02 at 170iterations 1.7877974E-03 3.2220840E-02 at 180iterations finished qdiffx linear iterations at : 08:37:24 total time elapsed so far: 11.69000 # loops : 180 mean,max change (kT/e) : 1.7877974E-03 3.2220840E-02 energy calculations done at 11.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 08:37:25 11.863u 0.173s 0:12.36 97.3% 0+0k 0+0io 0pf+0w