Mon Oct 10 11:06:33 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+sph.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 = amb.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 11:06:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5011191 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): 43.56300 114.6040 ymin,ymax (A): -25.27600 39.64000 zmin,zma (A): -32.78500 33.83900 x,y,z range (A): 71.04100 64.91600 66.62399 scale (grids/A): 0.5011191 object centre (A): 79.08350 7.182002 0.5269985 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 7.500055 assigned positive charge : 843.2379 centred at (gu) : 90.55933 89.38722 91.05011 assigned negative charge : -835.7458 centred at (gu) : 90.52759 89.40462 91.05915 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8533 nv = 96 ne = 84 npr = 105469 no. pairs analyzed = 105469 no. exposed pairs = 6422 no. arc points = 43610 no. surface atoms = 2155 nbur = 3194 mkacc time = 0.2200000 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 = 1.736000 m= 286 mr = 4670 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4290 ## 657 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 11465 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5883944E-11 6.6104795E-11 midg,1,midg; midg,igrid,midg 1.2165362E-10 2.8883446E-11 1,midg,midg; igrid,midg,midg 4.3818751E-12 1.5322973E-10 gauss-seidel spectral radius is 0.9796751 estimated iterations to convergence 58 setup time was (sec) 0.6800000 now iterating at: 11:06:34 rms-change max change #iterations 6.5605305E-02 9.108437 at 10iterations 3.5427024E-03 0.4744453 at 20iterations 4.6635896E-04 7.1827888E-02 at 30iterations 2.1603804E-04 3.4328341E-02 at 40iterations 1.1120796E-04 1.7590284E-02 at 50iterations finished qdiffx linear iterations at : 11:06:36 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.1120796E-04 1.7590284E-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) 3.460000 DelPhi exited at 11:06:37 3.466u 0.250s 0:04.12 90.0% 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 Mon Oct 10 2011 at 11:06:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.503357 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): 43.56300 114.6040 ymin,ymax (A): -25.27600 39.64000 zmin,zma (A): -32.78500 33.83900 x,y,z range (A): 71.04100 64.91600 66.62399 scale (grids/A): 1.503357 object centre (A): 79.08350 7.182002 0.5269985 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 7.500055 assigned positive charge : 843.2379 centred at (gu) : 91.67642 88.16035 93.14877 assigned negative charge : -835.7458 centred at (gu) : 91.58289 88.21400 93.17728 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 98972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43610 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 28408 mr = 70506 m= 2261 mr = 19346 m= 29 mr = 965 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1870 time to turn everything in is 0.6700000 number of dielectric boundary points 38853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 607 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 38625 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) : 0.5011191 object centre at (A) : 79.08350 7.182002 0.5269985 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2800768E-03 -3.6340102E-03 midg,1,midg; midg,igrid,midg 1.2287374E-02 -1.5437083E-03 1,midg,midg; igrid,midg,midg -2.3601759E-02 9.1967750E-03 gauss-seidel spectral radius is 0.9980733 estimated iterations to convergence 181 setup time was (sec) 0.9600000 now iterating at: 11:06:38 rms-change max change #iterations 3.943667 149.3614 at 10iterations 1.598852 54.11224 at 20iterations 0.6506141 19.90769 at 30iterations 0.2648208 8.733177 at 40iterations 0.1079075 3.293558 at 50iterations 4.3899313E-02 1.341553 at 60iterations 1.7889896E-02 0.5139885 at 70iterations 7.3459614E-03 0.2790060 at 80iterations 3.0309914E-03 8.8951111E-02 at 90iterations 1.3150510E-03 4.4887543E-02 at 100iterations 6.4127456E-04 2.2241592E-02 at 110iterations 3.8145669E-04 1.3866425E-02 at 120iterations finished qdiffx linear iterations at : 11:06:45 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 3.8145669E-04 1.3866425E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 11:06:45 7.672u 0.255s 0:08.29 95.5% 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 Mon Oct 10 2011 at 11:06:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.255036 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): 43.56300 114.6040 ymin,ymax (A): -25.27600 39.64000 zmin,zma (A): -32.78500 33.83900 x,y,z range (A): 71.04100 64.91600 66.62399 scale (grids/A): 2.255036 object centre (A): 79.08350 7.182002 0.5269985 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 7.500055 assigned positive charge : 843.2379 centred at (gu) : 92.51385 87.24007 94.72270 assigned negative charge : -835.7458 centred at (gu) : 92.37428 87.32098 94.76571 start vw surface at 0.2000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 231136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43610 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 104240 mr = 172805 m= 24888 mr = 82905 m= 3109 mr = 18174 m= 144 mr = 1918 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 6303 time to turn everything in is 1.600000 number of dielectric boundary points 87665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 41391 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) : 1.503357 object centre at (A) : 79.08350 7.182002 0.5269985 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6780953E-02 -0.2178012 midg,1,midg; midg,igrid,midg 0.3191497 -5.8669236E-02 1,midg,midg; igrid,midg,midg -0.7673048 0.1563180 gauss-seidel spectral radius is 0.9991523 estimated iterations to convergence 271 setup time was (sec) 1.910000 now iterating at: 11:06:47 rms-change max change #iterations 10.81376 279.3145 at 10iterations 6.174787 158.9206 at 20iterations 3.498547 75.20587 at 30iterations 1.969625 41.05808 at 40iterations 1.102126 21.27994 at 50iterations 0.6159200 12.57354 at 60iterations 0.3430154 6.471130 at 70iterations 0.1909531 3.459265 at 80iterations 0.1061425 1.892819 at 90iterations 5.8921702E-02 1.032120 at 100iterations 3.2710649E-02 0.5661769 at 110iterations 1.8140066E-02 0.3854618 at 120iterations 1.0045169E-02 0.1878204 at 130iterations 5.5834386E-03 0.1063979 at 140iterations 3.1089357E-03 5.8685303E-02 at 150iterations 1.7401108E-03 3.1474113E-02 at 160iterations 9.8960439E-04 2.0599365E-02 at 170iterations 5.8205455E-04 1.3710022E-02 at 180iterations finished qdiffx linear iterations at : 11:06:58 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 5.8205455E-04 1.3710022E-02 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 11:06:59 12.616u 0.261s 0:13.18 97.6% 0+0k 0+0io 0pf+0w