Mon Oct 10 17:09:46 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 17:09:46 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 = 2826 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: 0.6176695 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): -26.08900 31.54700 ymin,ymax (A): -10.10200 41.00200 zmin,zma (A): 4.707000 60.20000 x,y,z range (A): 57.63600 51.10400 55.49300 scale (grids/A): 0.6176695 object centre (A): 2.729001 15.45000 32.45350 number of atom coordinates read : 2826 total number of charged atoms : 2684 net assigned charge : -1.999968 assigned positive charge : 423.9562 centred at (gu) : 91.00875 90.41411 91.41344 assigned negative charge : -425.9573 centred at (gu) : 91.11674 90.30656 91.44697 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7170 nv = 96 ne = 84 npr = 56281 no. pairs analyzed = 56281 no. exposed pairs = 3829 no. arc points = 26807 no. surface atoms = 1281 nbur = 1545 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3680 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.3200000 number of dielectric boundary points 3839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2684 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8871 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1515404E-10 -5.0488596E-09 midg,1,midg; midg,igrid,midg -8.0200131E-09 6.3956120E-09 1,midg,midg; igrid,midg,midg 4.6514455E-09 -1.1073790E-08 gauss-seidel spectral radius is 0.9864526 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 17:09:47 rms-change max change #iterations 0.1271960 19.98764 at 10iterations 1.1620243E-02 1.675437 at 20iterations 1.0781864E-03 0.1432323 at 30iterations 1.0498874E-04 1.7704010E-02 at 40iterations 1.3775102E-05 2.7637482E-03 at 50iterations finished qdiffx linear iterations at : 17:09:50 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.3775102E-05 2.7637482E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 17:09:51 4.259u 0.252s 0:04.85 92.7% 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 17:09:51 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 = 2826 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: 1.853009 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): -26.08900 31.54700 ymin,ymax (A): -10.10200 41.00200 zmin,zma (A): 4.707000 60.20000 x,y,z range (A): 57.63600 51.10400 55.49300 scale (grids/A): 1.853009 object centre (A): 2.729001 15.45000 32.45350 number of atom coordinates read : 2826 total number of charged atoms : 2684 net assigned charge : -1.999968 assigned positive charge : 423.9562 centred at (gu) : 93.02544 91.24181 94.23942 assigned negative charge : -425.9573 centred at (gu) : 93.35011 90.91960 94.34057 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26807 grid for indexing accessible points = 1.400000 m= 26595 mr = 51613 m= 3875 mr = 18739 m= 183 mr = 2296 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1388 time to turn everything in is 0.5900000 number of dielectric boundary points 35505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21045 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) : 0.6176695 object centre at (A) : 2.729001 15.45000 32.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0467427E-03 1.6612338E-02 midg,1,midg; midg,igrid,midg -2.8852623E-02 5.8051362E-03 1,midg,midg; igrid,midg,midg 2.7154930E-02 -5.6099530E-02 gauss-seidel spectral radius is 0.9985873 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 17:09:52 rms-change max change #iterations 4.229725 202.5694 at 10iterations 1.950548 62.78850 at 20iterations 0.8963258 30.69470 at 30iterations 0.4139758 14.68976 at 40iterations 0.1905087 6.944893 at 50iterations 8.8000551E-02 2.856947 at 60iterations 4.0403590E-02 1.356607 at 70iterations 1.8733200E-02 0.6007957 at 80iterations 8.6561767E-03 0.3039026 at 90iterations 3.9922162E-03 0.1414261 at 100iterations 1.8490118E-03 5.8090210E-02 at 110iterations 8.5311045E-04 3.0342102E-02 at 120iterations finished qdiffx linear iterations at : 17:10:01 total time elapsed so far: 9.530000 # loops : 120 mean,max change (kT/e) : 8.5311045E-04 3.0342102E-02 energy calculations done at 9.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 17:10:01 9.718u 0.303s 0:10.43 95.9% 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 17:10:01 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 = 2826 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: 2.779513 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): -26.08900 31.54700 ymin,ymax (A): -10.10200 41.00200 zmin,zma (A): 4.707000 60.20000 x,y,z range (A): 57.63600 51.10400 55.49300 scale (grids/A): 2.779513 object centre (A): 2.729001 15.45000 32.45350 number of atom coordinates read : 2826 total number of charged atoms : 2684 net assigned charge : -1.999968 assigned positive charge : 423.9562 centred at (gu) : 94.53790 91.86255 96.35885 assigned negative charge : -425.9573 centred at (gu) : 95.02528 91.37922 96.51064 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 179270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26807 grid for indexing accessible points = 1.400000 m= 86347 mr = 125809 m= 30168 mr = 68607 m= 6673 mr = 23561 m= 756 mr = 4853 m= 31 mr = 503 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 4776 time to turn everything in is 1.520000 number of dielectric boundary points 79912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 21471 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) : 1.853009 object centre at (A) : 2.729001 15.45000 32.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1313240E-03 0.3587475 midg,1,midg; midg,igrid,midg -0.2598313 5.5557694E-02 1,midg,midg; igrid,midg,midg 0.3712929 -0.7265437 gauss-seidel spectral radius is 0.9992631 estimated iterations to convergence 291 setup time was (sec) 1.880000 now iterating at: 17:10:04 rms-change max change #iterations 10.28209 360.1751 at 10iterations 6.087533 175.7968 at 20iterations 3.578917 85.52493 at 30iterations 2.085978 42.84286 at 40iterations 1.214020 25.97685 at 50iterations 0.7039688 16.84942 at 60iterations 0.4075374 8.875561 at 70iterations 0.2355962 5.128321 at 80iterations 0.1360023 2.823237 at 90iterations 7.8328133E-02 1.482624 at 100iterations 4.5175072E-02 0.9046493 at 110iterations 2.6051037E-02 0.5472412 at 120iterations 1.4986213E-02 0.2994990 at 130iterations 8.6359382E-03 0.1614990 at 140iterations 4.9758013E-03 9.4104767E-02 at 150iterations 2.8586416E-03 5.6076050E-02 at 160iterations 1.6458103E-03 3.7648201E-02 at 170iterations 9.4950042E-04 1.8153906E-02 at 180iterations finished qdiffx linear iterations at : 17:10:17 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 9.4950042E-04 1.8153906E-02 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 17:10:18 15.941u 0.305s 0:16.56 98.0% 0+0k 0+0io 0pf+0w