Tue Oct 11 06:02:29 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 Tue Oct 11 2011 at 06:02:29 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7081195 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): 25.79900 72.25500 ymin,ymax (A): -18.77300 31.50100 zmin,zma (A): 3.996000 46.31400 x,y,z range (A): 46.45600 50.27400 42.31800 scale (grids/A): 0.7081195 object centre (A): 49.02700 6.364000 25.15500 number of atom coordinates read : 2339 total number of charged atoms : 2013 net assigned charge : 6.500009 assigned positive charge : 327.7008 centred at (gu) : 89.30312 90.29263 90.30817 assigned negative charge : -321.2010 centred at (gu) : 89.43468 90.24510 90.38832 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7203 nv = 96 ne = 84 npr = 42934 no. pairs analyzed = 42934 no. exposed pairs = 2580 no. arc points = 17637 no. surface atoms = 881 nbur = 1458 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4161 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1622 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8032 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0857320E-08 1.4201443E-08 midg,1,midg; midg,igrid,midg 2.9082422E-08 8.4358703E-08 1,midg,midg; igrid,midg,midg 1.4024270E-07 -1.1421710E-08 gauss-seidel spectral radius is 0.9896069 estimated iterations to convergence 80 setup time was (sec) 0.3700000 now iterating at: 06:02:29 rms-change max change #iterations 0.2024846 34.39967 at 10iterations 2.5510278E-02 3.447730 at 20iterations 3.2618942E-03 0.4838543 at 30iterations 5.1754131E-04 8.3267212E-02 at 40iterations 1.2393789E-04 1.6624451E-02 at 50iterations finished qdiffx linear iterations at : 06:02:32 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.2393789E-04 1.6624451E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 06:02:33 3.436u 0.164s 0:03.97 90.4% 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 06:02:33 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.124359 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): 25.79900 72.25500 ymin,ymax (A): -18.77300 31.50100 zmin,zma (A): 3.996000 46.31400 x,y,z range (A): 46.45600 50.27400 42.31800 scale (grids/A): 2.124359 object centre (A): 49.02700 6.364000 25.15500 number of atom coordinates read : 2339 total number of charged atoms : 2013 net assigned charge : 6.500009 assigned positive charge : 327.7008 centred at (gu) : 87.90945 90.87772 90.92432 assigned negative charge : -321.2010 centred at (gu) : 88.30392 90.73537 91.16502 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76523 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17637 grid for indexing accessible points = 1.400000 m= 31071 mr = 54689 m= 6021 mr = 23738 m= 561 mr = 4087 m= 13 mr = 288 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 31387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15956 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) : 0.7081195 object centre at (A) : 49.02700 6.364000 25.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2359632E-02 2.9182006E-02 midg,1,midg; midg,igrid,midg 4.5839891E-02 2.7224557E-02 1,midg,midg; igrid,midg,midg 4.6016876E-02 -4.7729496E-02 gauss-seidel spectral radius is 0.9988353 estimated iterations to convergence 232 setup time was (sec) 0.6300000 now iterating at: 06:02:34 rms-change max change #iterations 4.694251 244.0348 at 10iterations 2.320467 82.56113 at 20iterations 1.154606 35.81561 at 30iterations 0.5741736 16.55203 at 40iterations 0.2859803 8.104001 at 50iterations 0.1418395 4.227888 at 60iterations 7.0554465E-02 1.982162 at 70iterations 3.5103191E-02 1.040852 at 80iterations 1.7480666E-02 0.5732079 at 90iterations 8.7583857E-03 0.2585220 at 100iterations 4.3930123E-03 0.1208696 at 110iterations 2.2449640E-03 7.3780060E-02 at 120iterations finished qdiffx linear iterations at : 06:02:41 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.2449640E-03 7.3780060E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 06:02:41 7.985u 0.186s 0:08.46 96.4% 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 06:02:41 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 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: 3.186538 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): 25.79900 72.25500 ymin,ymax (A): -18.77300 31.50100 zmin,zma (A): 3.996000 46.31400 x,y,z range (A): 46.45600 50.27400 42.31800 scale (grids/A): 3.186538 object centre (A): 49.02700 6.364000 25.15500 number of atom coordinates read : 2339 total number of charged atoms : 2013 net assigned charge : 6.500009 assigned positive charge : 327.7008 centred at (gu) : 86.86401 91.31663 91.38650 assigned negative charge : -321.2010 centred at (gu) : 87.45589 91.10305 91.74739 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 176279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17637 grid for indexing accessible points = 1.400000 m= 96654 mr = 131475 m= 39425 mr = 80806 m= 11444 mr = 32567 m= 2305 mr = 8995 m= 271 mr = 1715 m= 15 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 70655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 16104 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) : 2.124359 object centre at (A) : 49.02700 6.364000 25.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1223802 0.2509757 midg,1,midg; midg,igrid,midg 0.3720071 0.1445159 1,midg,midg; igrid,midg,midg 0.4397556 -0.5912213 gauss-seidel spectral radius is 0.9992970 estimated iterations to convergence 298 setup time was (sec) 1.430000 now iterating at: 06:02:43 rms-change max change #iterations 10.42231 390.6452 at 10iterations 6.166839 133.6764 at 20iterations 3.644670 80.15155 at 30iterations 2.149031 44.23272 at 40iterations 1.264458 23.32456 at 50iterations 0.7434026 13.80574 at 60iterations 0.4360230 7.998573 at 70iterations 0.2567616 4.847853 at 80iterations 0.1504248 2.918131 at 90iterations 8.8214748E-02 1.637369 at 100iterations 5.1775686E-02 0.9509453 at 110iterations 3.0451007E-02 0.5433731 at 120iterations 1.8028559E-02 0.3127289 at 130iterations 1.0762178E-02 0.1836128 at 140iterations 6.5681585E-03 0.1178322 at 150iterations 4.1199904E-03 7.7533722E-02 at 160iterations 2.7033838E-03 4.5928955E-02 at 170iterations 1.8814538E-03 3.2424927E-02 at 180iterations finished qdiffx linear iterations at : 06:02:54 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 1.8814538E-03 3.2424927E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 06:02:55 12.963u 0.231s 0:13.89 94.9% 0+0k 0+0io 0pf+0w