Sat Oct 8 17:21:51 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 Sat Oct 8 2011 at 17:21:51 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 = 3471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5565631 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): 165.4820 229.4460 ymin,ymax (A): -25.00200 29.06200 zmin,zma (A): -3.215000 51.02800 x,y,z range (A): 63.96399 54.06400 54.24300 scale (grids/A): 0.5565631 object centre (A): 197.4640 2.030001 23.90650 number of atom coordinates read : 3471 total number of charged atoms : 3324 net assigned charge : -6.999965 assigned positive charge : 518.5672 centred at (gu) : 92.10688 88.56314 88.85809 assigned negative charge : -525.5689 centred at (gu) : 92.10352 88.55939 88.82581 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6990 nv = 96 ne = 84 npr = 69876 no. pairs analyzed = 69876 no. exposed pairs = 4538 no. arc points = 30885 no. surface atoms = 1528 nbur = 1943 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= 330 mr = 3700 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3112 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9143 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3383825E-09 -2.1426769E-10 midg,1,midg; midg,igrid,midg -9.6743036E-10 -4.3010520E-10 1,midg,midg; igrid,midg,midg -4.1741327E-10 -9.9894581E-10 gauss-seidel spectral radius is 0.9833854 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 17:21:51 rms-change max change #iterations 8.9312218E-02 15.51620 at 10iterations 6.4047561E-03 0.9255600 at 20iterations 6.3139538E-04 9.2603683E-02 at 30iterations 1.4875538E-04 2.6897430E-02 at 40iterations 4.7617734E-05 8.8682175E-03 at 50iterations finished qdiffx linear iterations at : 17:21:54 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 4.7617734E-05 8.8682175E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 17:21:54 3.180u 0.138s 0:03.58 92.4% 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 Sat Oct 8 2011 at 17:21:54 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 = 3471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.669690 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): 165.4820 229.4460 ymin,ymax (A): -25.00200 29.06200 zmin,zma (A): -3.215000 51.02800 x,y,z range (A): 63.96399 54.06400 54.24300 scale (grids/A): 1.669690 object centre (A): 197.4640 2.030001 23.90650 number of atom coordinates read : 3471 total number of charged atoms : 3324 net assigned charge : -6.999965 assigned positive charge : 518.5672 centred at (gu) : 96.31966 85.68855 86.57307 assigned negative charge : -525.5689 centred at (gu) : 96.31010 85.67775 86.47693 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30885 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26588 mr = 53346 m= 3304 mr = 18698 m= 112 mr = 1749 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 150 time to turn everything in is 0.5500000 number of dielectric boundary points 33426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25527 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) : 0.5565631 object centre at (A) : 197.4640 2.030001 23.90650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6940840E-03 -1.5255923E-02 midg,1,midg; midg,igrid,midg -1.4462437E-02 1.9505960E-03 1,midg,midg; igrid,midg,midg 4.5014699E-03 4.2090039E-03 gauss-seidel spectral radius is 0.9983065 estimated iterations to convergence 193 setup time was (sec) 0.8400000 now iterating at: 17:21:55 rms-change max change #iterations 3.830753 187.0986 at 10iterations 1.635774 60.14721 at 20iterations 0.7029491 21.92188 at 30iterations 0.3005798 9.791817 at 40iterations 0.1293987 4.282291 at 50iterations 5.5629019E-02 1.762302 at 60iterations 2.3929939E-02 0.7845764 at 70iterations 1.0358516E-02 0.3412952 at 80iterations 4.4997702E-03 0.1470718 at 90iterations 1.9502980E-03 6.0916901E-02 at 100iterations 8.7791728E-04 2.8591156E-02 at 110iterations 4.1278999E-04 1.4481544E-02 at 120iterations finished qdiffx linear iterations at : 17:22:01 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 4.1278999E-04 1.4481544E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 17:22:02 7.028u 0.123s 0:07.42 96.2% 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 Sat Oct 8 2011 at 17:22:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3471 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.504534 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): 165.4820 229.4460 ymin,ymax (A): -25.00200 29.06200 zmin,zma (A): -3.215000 51.02800 x,y,z range (A): 63.96399 54.06400 54.24300 scale (grids/A): 2.504534 object centre (A): 197.4640 2.030001 23.90650 number of atom coordinates read : 3471 total number of charged atoms : 3324 net assigned charge : -6.999965 assigned positive charge : 518.5672 centred at (gu) : 99.47922 83.53237 84.85931 assigned negative charge : -525.5689 centred at (gu) : 99.46507 83.51659 84.71536 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 179206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30885 grid for indexing accessible points = 1.400000 m= 88404 mr = 130208 m= 28599 mr = 70531 m= 5393 mr = 22061 m= 459 mr = 3597 m= 10 mr = 238 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 525 time to turn everything in is 1.300000 number of dielectric boundary points 75436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 26559 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) : 1.669690 object centre at (A) : 197.4640 2.030001 23.90650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9513925E-03 -0.1957524 midg,1,midg; midg,igrid,midg -0.1958966 3.6933366E-02 1,midg,midg; igrid,midg,midg 0.1194836 0.2311583 gauss-seidel spectral radius is 0.9991817 estimated iterations to convergence 276 setup time was (sec) 1.570000 now iterating at: 17:22:04 rms-change max change #iterations 9.794907 361.7468 at 10iterations 5.629848 138.8946 at 20iterations 3.220391 70.22926 at 30iterations 1.826509 39.07096 at 40iterations 1.032472 20.52381 at 50iterations 0.5817002 11.08229 at 60iterations 0.3271254 6.687843 at 70iterations 0.1839233 3.540409 at 80iterations 0.1030737 1.918379 at 90iterations 5.7839457E-02 1.030401 at 100iterations 3.2337207E-02 0.6451359 at 110iterations 1.8132703E-02 0.3292027 at 120iterations 1.0156838E-02 0.1965771 at 130iterations 5.6577763E-03 0.1193743 at 140iterations 3.1756575E-03 5.9616089E-02 at 150iterations 1.7734336E-03 3.2247543E-02 at 160iterations 9.9162105E-04 1.8264771E-02 at 170iterations 5.5469444E-04 1.1394501E-02 at 180iterations finished qdiffx linear iterations at : 17:22:13 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 5.5469444E-04 1.1394501E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 17:22:14 11.303u 0.177s 0:11.80 97.2% 0+0k 0+0io 0pf+0w