Mon Oct 10 14:00:31 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 Mon Oct 10 2011 at 14:00:31 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4044 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 0.5552782 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): -3.525000 60.58700 ymin,ymax (A): -12.50500 38.86300 zmin,zma (A): -17.26500 45.29100 x,y,z range (A): 64.11200 51.36800 62.55600 scale (grids/A): 0.5552782 object centre (A): 28.53100 13.17900 14.01300 number of atom coordinates read : 4044 total number of charged atoms : 3886 net assigned charge : -3.485937 assigned positive charge : 602.0753 centred at (gu) : 89.17653 90.27066 90.57690 assigned negative charge : -605.5634 centred at (gu) : 89.21598 90.36208 90.67310 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8001 nv = 96 ne = 84 npr = 85502 no. pairs analyzed = 85502 no. exposed pairs = 4579 no. arc points = 30614 no. surface atoms = 1570 nbur = 2474 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 = 1.540000 m= 315 mr = 4615 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3183 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 10604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8583262E-10 -1.7779163E-09 midg,1,midg; midg,igrid,midg 7.9283463E-10 -1.5816558E-09 1,midg,midg; igrid,midg,midg 2.4638272E-10 -6.6114464E-10 gauss-seidel spectral radius is 0.9833447 estimated iterations to convergence 64 setup time was (sec) 0.4600000 now iterating at: 14:00:31 rms-change max change #iterations 9.7549319E-02 12.94674 at 10iterations 8.6892294E-03 1.334584 at 20iterations 1.7541058E-03 0.1967316 at 30iterations 5.5334537E-04 5.2949905E-02 at 40iterations 1.8424584E-04 1.9468307E-02 at 50iterations finished qdiffx linear iterations at : 14:00:34 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.8424584E-04 1.9468307E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:00:35 3.444u 0.174s 0:04.19 86.1% 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 Mon Oct 10 2011 at 14:00:35 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4044 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 1.665835 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): -3.525000 60.58700 ymin,ymax (A): -12.50500 38.86300 zmin,zma (A): -17.26500 45.29100 x,y,z range (A): 64.11200 51.36800 62.55600 scale (grids/A): 1.665835 object centre (A): 28.53100 13.17900 14.01300 number of atom coordinates read : 4044 total number of charged atoms : 3886 net assigned charge : -3.485937 assigned positive charge : 602.0753 centred at (gu) : 87.52821 90.81121 91.72974 assigned negative charge : -605.5634 centred at (gu) : 87.64743 91.08588 92.01901 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 90158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30614 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30023 mr = 65985 m= 3377 mr = 21771 m= 100 mr = 1894 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 373 time to turn everything in is 0.4200000 number of dielectric boundary points 34001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 305 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 29959 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) : 0.5552782 object centre at (A) : 28.53100 13.17900 14.01300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2384899E-02 -1.6188717E-02 midg,1,midg; midg,igrid,midg 3.9910455E-03 -2.2188015E-02 1,midg,midg; igrid,midg,midg 1.4395793E-02 2.2710679E-02 gauss-seidel spectral radius is 0.9983540 estimated iterations to convergence 196 setup time was (sec) 0.6300000 now iterating at: 14:00:36 rms-change max change #iterations 4.139956 152.6749 at 10iterations 1.803509 57.42273 at 20iterations 0.7851132 24.28029 at 30iterations 0.3429039 11.03516 at 40iterations 0.1498798 4.454563 at 50iterations 6.5649994E-02 2.037315 at 60iterations 2.9044127E-02 1.003395 at 70iterations 1.2963380E-02 0.3820877 at 80iterations 5.9739682E-03 0.1900253 at 90iterations 2.9245254E-03 8.9630127E-02 at 100iterations 1.5351538E-03 4.4773102E-02 at 110iterations 8.8321505E-04 2.1640778E-02 at 120iterations finished qdiffx linear iterations at : 14:00:43 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 8.8321505E-04 2.1640778E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 14:00:44 7.795u 0.247s 0:09.24 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 Mon Oct 10 2011 at 14:00:44 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4044 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 2.498752 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): -3.525000 60.58700 ymin,ymax (A): -12.50500 38.86300 zmin,zma (A): -17.26500 45.29100 x,y,z range (A): 64.11200 51.36800 62.55600 scale (grids/A): 2.498752 object centre (A): 28.53100 13.17900 14.01300 number of atom coordinates read : 4044 total number of charged atoms : 3886 net assigned charge : -3.485937 assigned positive charge : 602.0753 centred at (gu) : 86.29206 91.21645 92.59411 assigned negative charge : -605.5634 centred at (gu) : 86.47105 91.62852 93.02855 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 210127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30614 grid for indexing accessible points = 1.400000 m= 103387 mr = 160713 m= 30995 mr = 84886 m= 5751 mr = 24025 m= 459 mr = 4025 m= 16 mr = 220 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1216 time to turn everything in is 1.060000 number of dielectric boundary points 76866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 31052 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) : 1.665835 object centre at (A) : 28.53100 13.17900 14.01300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5167014 -0.2824871 midg,1,midg; midg,igrid,midg 7.3263913E-02 -0.3010458 1,midg,midg; igrid,midg,midg 0.3546668 0.4142756 gauss-seidel spectral radius is 0.9992070 estimated iterations to convergence 280 setup time was (sec) 1.290000 now iterating at: 14:00:46 rms-change max change #iterations 10.50089 315.2013 at 10iterations 6.036470 132.7576 at 20iterations 3.458164 65.20170 at 30iterations 1.972063 36.55355 at 40iterations 1.123888 18.88544 at 50iterations 0.6378520 11.51905 at 60iterations 0.3621491 7.280718 at 70iterations 0.2050987 3.521927 at 80iterations 0.1162170 2.132767 at 90iterations 6.5776065E-02 1.142254 at 100iterations 3.7322551E-02 0.7291565 at 110iterations 2.1239631E-02 0.4056129 at 120iterations 1.2164559E-02 0.2103081 at 130iterations 7.0323176E-03 0.1342545 at 140iterations 4.1609956E-03 7.7040672E-02 at 150iterations 2.5421025E-03 4.3621063E-02 at 160iterations 1.6195955E-03 2.7286530E-02 at 170iterations 1.0884661E-03 1.6698837E-02 at 180iterations finished qdiffx linear iterations at : 14:00:57 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 1.0884661E-03 1.6698837E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 14:00:58 12.592u 0.219s 0:13.91 92.0% 0+0k 0+0io 0pf+0w