Mon Oct 10 09:14:02 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 09:14:02 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6544719 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): -6.294000 34.32100 ymin,ymax (A): -3.365000 48.58800 zmin,zma (A): -23.45700 30.93800 x,y,z range (A): 40.61500 51.95300 54.39500 scale (grids/A): 0.6544719 object centre (A): 14.01350 22.61150 3.740500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.6259 centred at (gu) : 90.96066 92.41437 89.95228 assigned negative charge : -289.6262 centred at (gu) : 91.06144 92.53899 89.90749 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5675 nv = 96 ne = 84 npr = 40489 no. pairs analyzed = 40489 no. exposed pairs = 2434 no. arc points = 17039 no. surface atoms = 824 nbur = 1140 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3204 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.1700000 number of dielectric boundary points 2748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1724 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3994325E-09 1.2634504E-08 midg,1,midg; midg,igrid,midg 1.3765880E-08 -1.5417379E-08 1,midg,midg; igrid,midg,midg 1.6168320E-08 -7.2625737E-09 gauss-seidel spectral radius is 0.9878423 estimated iterations to convergence 74 setup time was (sec) 0.3500000 now iterating at: 09:14:02 rms-change max change #iterations 0.1447395 26.29431 at 10iterations 1.5185827E-02 2.086250 at 20iterations 1.5584187E-03 0.2433481 at 30iterations 1.5821232E-04 2.5148392E-02 at 40iterations 1.6711776E-05 2.5024414E-03 at 50iterations finished qdiffx linear iterations at : 09:14:05 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.6711776E-05 2.5024414E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 09:14:06 3.353u 0.171s 0:03.91 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 09:14:06 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.963416 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): -6.294000 34.32100 ymin,ymax (A): -3.365000 48.58800 zmin,zma (A): -23.45700 30.93800 x,y,z range (A): 40.61500 51.95300 54.39500 scale (grids/A): 1.963416 object centre (A): 14.01350 22.61150 3.740500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.6259 centred at (gu) : 92.88182 97.24298 89.85680 assigned negative charge : -289.6262 centred at (gu) : 93.18449 97.61707 89.72262 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 61340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17039 grid for indexing accessible points = 1.400000 m= 22577 mr = 42570 m= 3583 mr = 17271 m= 184 mr = 2338 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1228 time to turn everything in is 0.3100000 number of dielectric boundary points 25462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14491 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) : 0.6544719 object centre at (A) : 14.01350 22.61150 3.740500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8413962E-02 1.6696224E-02 midg,1,midg; midg,igrid,midg 3.6784004E-02 -6.2853470E-03 1,midg,midg; igrid,midg,midg 1.1244372E-02 -6.9242301E-03 gauss-seidel spectral radius is 0.9986335 estimated iterations to convergence 214 setup time was (sec) 0.5300000 now iterating at: 09:14:06 rms-change max change #iterations 3.864638 212.9485 at 10iterations 1.818592 65.17975 at 20iterations 0.8516461 30.32077 at 30iterations 0.3971736 13.78013 at 40iterations 0.1856107 6.954710 at 50iterations 8.6803794E-02 3.097543 at 60iterations 4.0770940E-02 1.472710 at 70iterations 1.9066179E-02 0.7085571 at 80iterations 8.9293551E-03 0.3065872 at 90iterations 4.1588517E-03 0.1387196 at 100iterations 1.9590051E-03 6.6970825E-02 at 110iterations 9.1422914E-04 3.0128479E-02 at 120iterations finished qdiffx linear iterations at : 09:14:13 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 9.1422914E-04 3.0128479E-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) 7.700000 DelPhi exited at 09:14:14 7.699u 0.185s 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 Mon Oct 10 2011 at 09:14:14 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.945124 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): -6.294000 34.32100 ymin,ymax (A): -3.365000 48.58800 zmin,zma (A): -23.45700 30.93800 x,y,z range (A): 40.61500 51.95300 54.39500 scale (grids/A): 2.945124 object centre (A): 14.01350 22.61150 3.740500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.6259 centred at (gu) : 94.32269 100.8644 89.78536 assigned negative charge : -289.6262 centred at (gu) : 94.77682 101.4255 89.58388 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 141501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17039 grid for indexing accessible points = 1.400000 m= 72254 mr = 102565 m= 26877 mr = 60157 m= 6627 mr = 22310 m= 893 mr = 5148 m= 29 mr = 567 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 4259 time to turn everything in is 0.7900000 number of dielectric boundary points 57432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14656 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) : 1.963416 object centre at (A) : 14.01350 22.61150 3.740500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9173344 5.7368185E-02 midg,1,midg; midg,igrid,midg 0.3474152 -0.1055598 1,midg,midg; igrid,midg,midg 8.2965821E-02 -4.8174430E-02 gauss-seidel spectral radius is 0.9992460 estimated iterations to convergence 287 setup time was (sec) 1.010000 now iterating at: 09:14:15 rms-change max change #iterations 8.926849 363.6663 at 10iterations 5.127852 130.9654 at 20iterations 2.919195 60.87463 at 30iterations 1.667588 32.27761 at 40iterations 0.9526283 20.04546 at 50iterations 0.5427238 9.871471 at 60iterations 0.3094447 5.950176 at 70iterations 0.1763354 3.758959 at 80iterations 0.1005489 2.408791 at 90iterations 5.7296921E-02 1.140699 at 100iterations 3.2692436E-02 0.6406174 at 110iterations 1.8691750E-02 0.3449688 at 120iterations 1.0611130E-02 0.2142825 at 130iterations 6.0532824E-03 0.1422119 at 140iterations 3.4474139E-03 7.2250366E-02 at 150iterations 1.9738812E-03 4.3834686E-02 at 160iterations 1.1250051E-03 2.1630287E-02 at 170iterations 6.4038858E-04 1.2328625E-02 at 180iterations finished qdiffx linear iterations at : 09:14:26 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 6.4038858E-04 1.2328625E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 09:14:27 12.226u 0.224s 0:12.75 97.5% 0+0k 0+0io 0pf+0w