Tue Oct 11 03:21:09 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 03:21:10 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3336 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: ASN 165 has a net charge of -0.2720 !!! WARNING: SEP 225 has a net charge of -0.4750 !!! WARNING: GLU 499 has a net charge of -0.2720 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: 0.5443841 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): 4.083000 69.47800 ymin,ymax (A): 31.77200 91.59000 zmin,zma (A): 24.33800 78.45700 x,y,z range (A): 65.39500 59.81800 54.11900 scale (grids/A): 0.5443841 object centre (A): 36.78050 61.68100 51.39750 number of atom coordinates read : 3336 total number of charged atoms : 3188 net assigned charge : -7.587981 assigned positive charge : 501.8575 centred at (gu) : 87.63834 92.05365 87.95953 assigned negative charge : -509.4467 centred at (gu) : 87.60548 92.05322 87.98325 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6322 nv = 96 ne = 84 npr = 68540 no. pairs analyzed = 68540 no. exposed pairs = 4140 no. arc points = 29100 no. surface atoms = 1402 nbur = 1934 mkacc time = 0.1100000 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 = 1.596000 m= 221 mr = 3291 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2953 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8299 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3220816E-10 -3.6766931E-10 midg,1,midg; midg,igrid,midg -2.6799585E-10 -7.0974909E-10 1,midg,midg; igrid,midg,midg -1.1966400E-09 -1.1959715E-10 gauss-seidel spectral radius is 0.9826270 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 03:21:10 rms-change max change #iterations 7.8445375E-02 12.81591 at 10iterations 5.2732807E-03 0.9867115 at 20iterations 4.3243371E-04 6.2370300E-02 at 30iterations 6.6924644E-05 1.2839317E-02 at 40iterations 1.6331833E-05 3.4797192E-03 at 50iterations finished qdiffx linear iterations at : 03:21:13 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.6331833E-05 3.4797192E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 03:21:13 3.443u 0.153s 0:03.90 92.0% 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 Tue Oct 11 2011 at 03:21:14 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3336 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: ASN 165 has a net charge of -0.2720 !!! WARNING: SEP 225 has a net charge of -0.4750 !!! WARNING: GLU 499 has a net charge of -0.2720 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: 1.633152 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): 4.083000 69.47800 ymin,ymax (A): 31.77200 91.59000 zmin,zma (A): 24.33800 78.45700 x,y,z range (A): 65.39500 59.81800 54.11900 scale (grids/A): 1.633152 object centre (A): 36.78050 61.68100 51.39750 number of atom coordinates read : 3336 total number of charged atoms : 3188 net assigned charge : -7.587981 assigned positive charge : 501.8575 centred at (gu) : 82.91422 96.16016 83.87743 assigned negative charge : -509.4467 centred at (gu) : 82.81594 96.15911 83.94910 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 69761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29100 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20830 mr = 47305 m= 1979 mr = 14321 m= 46 mr = 885 m= 0 mr = 3 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 0.3600000 number of dielectric boundary points 30102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 390 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 24345 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) : 0.5443841 object centre at (A) : 36.78050 61.68100 51.39750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4804195E-03 -3.4363109E-03 midg,1,midg; midg,igrid,midg -3.8699401E-03 -5.1061679E-03 1,midg,midg; igrid,midg,midg -1.5941273E-02 2.6528195E-02 gauss-seidel spectral radius is 0.9982070 estimated iterations to convergence 188 setup time was (sec) 0.5800000 now iterating at: 03:21:14 rms-change max change #iterations 3.567564 155.6973 at 10iterations 1.492963 58.55054 at 20iterations 0.6255137 21.93530 at 30iterations 0.2612641 9.404799 at 40iterations 0.1100838 3.713938 at 50iterations 4.6039537E-02 1.819779 at 60iterations 1.9348789E-02 0.7192688 at 70iterations 8.1071900E-03 0.2813087 at 80iterations 3.4220917E-03 0.1127682 at 90iterations 1.4428647E-03 4.9939156E-02 at 100iterations 6.1435736E-04 2.0034790E-02 at 110iterations 2.6555388E-04 1.0242939E-02 at 120iterations finished qdiffx linear iterations at : 03:21:21 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 2.6555388E-04 1.0242939E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 03:21:22 7.697u 0.184s 0:08.19 96.0% 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 Tue Oct 11 2011 at 03:21:22 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3336 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: ASN 165 has a net charge of -0.2720 !!! WARNING: SEP 225 has a net charge of -0.4750 !!! WARNING: GLU 499 has a net charge of -0.2720 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: 2.449728 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): 4.083000 69.47800 ymin,ymax (A): 31.77200 91.59000 zmin,zma (A): 24.33800 78.45700 x,y,z range (A): 65.39500 59.81800 54.11900 scale (grids/A): 2.449728 object centre (A): 36.78050 61.68100 51.39750 number of atom coordinates read : 3336 total number of charged atoms : 3188 net assigned charge : -7.587981 assigned positive charge : 501.8575 centred at (gu) : 79.37107 99.24006 80.81596 assigned negative charge : -509.4467 centred at (gu) : 79.22388 99.23857 80.92374 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29100 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73342 mr = 115809 m= 19515 mr = 57943 m= 2934 mr = 14537 m= 178 mr = 1852 m= 5 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2255 time to turn everything in is 0.8400000 number of dielectric boundary points 67990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 25473 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) : 1.633152 object centre at (A) : 36.78050 61.68100 51.39750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1937477E-02 -6.6402964E-02 midg,1,midg; midg,igrid,midg -7.8554526E-03 -5.0636549E-03 1,midg,midg; igrid,midg,midg -0.3502141 0.5155889 gauss-seidel spectral radius is 0.9991495 estimated iterations to convergence 271 setup time was (sec) 1.080000 now iterating at: 03:21:23 rms-change max change #iterations 9.237153 315.1587 at 10iterations 5.218293 130.3068 at 20iterations 2.924863 82.88713 at 30iterations 1.633770 38.58967 at 40iterations 0.9090911 18.58938 at 50iterations 0.5055316 11.22739 at 60iterations 0.2802024 5.750965 at 70iterations 0.1551838 3.809910 at 80iterations 8.5973501E-02 1.645030 at 90iterations 4.7553539E-02 0.9900932 at 100iterations 2.6231242E-02 0.5424132 at 110iterations 1.4501383E-02 0.2903366 at 120iterations 8.0629662E-03 0.1580305 at 130iterations 4.4642957E-03 9.3757629E-02 at 140iterations 2.4801805E-03 4.8793793E-02 at 150iterations 1.3826031E-03 3.0190945E-02 at 160iterations 7.8099762E-04 1.6296387E-02 at 170iterations 4.4808708E-04 1.0627031E-02 at 180iterations finished qdiffx linear iterations at : 03:21:34 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 4.4808708E-04 1.0627031E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 03:21:35 12.399u 0.186s 0:12.87 97.6% 0+0k 0+0io 0pf+0w