Sun Oct 9 08:14:23 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 Sun Oct 9 2011 at 08:14:23 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 !!! WARNING: NAP 1048 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5502658 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): -24.82200 22.37000 ymin,ymax (A): -22.06600 36.63400 zmin,zma (A): -17.01900 47.67700 x,y,z range (A): 47.19200 58.70000 64.69600 scale (grids/A): 0.5502658 object centre (A): -1.226001 7.284001 15.32900 number of atom coordinates read : 3475 total number of charged atoms : 3335 net assigned charge : 10.50003 assigned positive charge : 521.1734 centred at (gu) : 89.63181 87.03521 90.07762 assigned negative charge : -510.6751 centred at (gu) : 89.68691 87.05048 90.11935 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6947 nv = 96 ne = 84 npr = 69204 no. pairs analyzed = 69204 no. exposed pairs = 4438 no. arc points = 31598 no. surface atoms = 1479 nbur = 1996 mkacc time = 0.1500000 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 = 1.568000 m= 311 mr = 3588 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3600000 number of dielectric boundary points 3658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3090 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8969 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1040624E-09 3.9323719E-10 midg,1,midg; midg,igrid,midg 1.8414463E-09 3.1308625E-10 1,midg,midg; igrid,midg,midg 1.3582211E-09 2.4628932E-10 gauss-seidel spectral radius is 0.9830139 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 08:14:24 rms-change max change #iterations 8.4404536E-02 13.29787 at 10iterations 5.9560579E-03 0.9453354 at 20iterations 5.5815448E-04 9.6199036E-02 at 30iterations 1.0955148E-04 1.4008522E-02 at 40iterations 2.9096926E-05 3.6935210E-03 at 50iterations finished qdiffx linear iterations at : 08:14:27 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.9096926E-05 3.6935210E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 08:14:27 3.526u 0.250s 0:04.06 92.8% 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 Sun Oct 9 2011 at 08:14:27 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 !!! WARNING: NAP 1048 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.650798 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): -24.82200 22.37000 ymin,ymax (A): -22.06600 36.63400 zmin,zma (A): -17.01900 47.67700 x,y,z range (A): 47.19200 58.70000 64.69600 scale (grids/A): 1.650798 object centre (A): -1.226001 7.284001 15.32900 number of atom coordinates read : 3475 total number of charged atoms : 3335 net assigned charge : 10.50003 assigned positive charge : 521.1734 centred at (gu) : 88.89471 81.10484 90.23201 assigned negative charge : -510.6751 centred at (gu) : 89.06069 81.15118 90.35790 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24585 mr = 52517 m= 2778 mr = 16852 m= 96 mr = 1367 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 819 time to turn everything in is 0.5700000 number of dielectric boundary points 33960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 25623 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) : 0.5502658 object centre at (A) : -1.226001 7.284001 15.32900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1059047E-02 -4.9903768E-04 midg,1,midg; midg,igrid,midg 2.0824850E-02 6.5378295E-03 1,midg,midg; igrid,midg,midg 1.5911657E-02 6.9251080E-04 gauss-seidel spectral radius is 0.9982834 estimated iterations to convergence 192 setup time was (sec) 0.8800000 now iterating at: 08:14:28 rms-change max change #iterations 3.715800 185.4449 at 10iterations 1.591642 57.26449 at 20iterations 0.6763735 23.02761 at 30iterations 0.2902066 10.40286 at 40iterations 0.1240735 3.900976 at 50iterations 5.2783061E-02 1.929013 at 60iterations 2.2653135E-02 0.7484589 at 70iterations 9.7316252E-03 0.3296547 at 80iterations 4.1816644E-03 0.1372089 at 90iterations 1.7967505E-03 6.0554504E-02 at 100iterations 7.7979069E-04 3.3926964E-02 at 110iterations 3.4406150E-04 1.2517929E-02 at 120iterations finished qdiffx linear iterations at : 08:14:35 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 3.4406150E-04 1.2517929E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 08:14:36 7.918u 0.270s 0:08.69 94.1% 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 Sun Oct 9 2011 at 08:14:36 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3475 !!! WARNING: NAP 1048 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.476196 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): -24.82200 22.37000 ymin,ymax (A): -22.06600 36.63400 zmin,zma (A): -17.01900 47.67700 x,y,z range (A): 47.19200 58.70000 64.69600 scale (grids/A): 2.476196 object centre (A): -1.226001 7.284001 15.32900 number of atom coordinates read : 3475 total number of charged atoms : 3335 net assigned charge : 10.50003 assigned positive charge : 521.1734 centred at (gu) : 88.34175 76.65699 90.34756 assigned negative charge : -510.6751 centred at (gu) : 88.59103 76.72665 90.53680 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 179697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84009 mr = 128824 m= 24907 mr = 66215 m= 4305 mr = 18624 m= 340 mr = 2789 m= 10 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 2772 time to turn everything in is 1.290000 number of dielectric boundary points 76676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 26644 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) : 1.650798 object centre at (A) : -1.226001 7.284001 15.32900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2540345 -2.9643914E-02 midg,1,midg; midg,igrid,midg 0.4161048 0.1247459 1,midg,midg; igrid,midg,midg 0.2004234 -2.3717184E-02 gauss-seidel spectral radius is 0.9991834 estimated iterations to convergence 276 setup time was (sec) 1.580000 now iterating at: 08:14:38 rms-change max change #iterations 9.626086 318.4138 at 10iterations 5.557640 138.6773 at 20iterations 3.182732 82.98727 at 30iterations 1.816352 44.28604 at 40iterations 1.027910 25.46747 at 50iterations 0.5802935 14.23714 at 60iterations 0.3272155 7.464364 at 70iterations 0.1842066 4.318192 at 80iterations 0.1036944 2.382135 at 90iterations 5.8093328E-02 1.339786 at 100iterations 3.2591999E-02 0.7260246 at 110iterations 1.8297043E-02 0.3724976 at 120iterations 1.0246619E-02 0.2189941 at 130iterations 5.7359049E-03 0.1105647 at 140iterations 3.2183505E-03 6.1989784E-02 at 150iterations 1.8012634E-03 4.0823936E-02 at 160iterations 1.0074603E-03 2.1504879E-02 at 170iterations 5.6501530E-04 1.2916565E-02 at 180iterations finished qdiffx linear iterations at : 08:14:47 total time elapsed so far: 11.52000 # loops : 180 mean,max change (kT/e) : 5.6501530E-04 1.2916565E-02 energy calculations done at 11.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 08:14:48 11.705u 0.172s 0:12.14 97.7% 0+0k 0+0io 0pf+0w