Sat Oct 8 18:35:33 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 Sat Oct 8 2011 at 18:35:33 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6376842 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): -31.66800 17.37000 ymin,ymax (A): -22.96200 23.09900 zmin,zma (A): -11.96800 43.85900 x,y,z range (A): 49.03800 46.06100 55.82700 scale (grids/A): 0.6376842 object centre (A): -7.149000 6.8499565E-02 15.94550 number of atom coordinates read : 2583 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 88.42815 88.94788 89.94529 assigned negative charge : -386.9045 centred at (gu) : 88.34857 89.01615 89.81542 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6842 nv = 96 ne = 84 npr = 54277 no. pairs analyzed = 54277 no. exposed pairs = 2909 no. arc points = 20930 no. surface atoms = 991 nbur = 1592 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 3949 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.3100000 number of dielectric boundary points 3192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2113 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8404 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2304856E-09 1.9883512E-08 midg,1,midg; midg,igrid,midg 1.7007666E-08 -9.5995489E-10 1,midg,midg; igrid,midg,midg -3.7498711E-09 1.0586892E-08 gauss-seidel spectral radius is 0.9872516 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 18:35:34 rms-change max change #iterations 0.1469320 21.13453 at 10iterations 1.4358125E-02 2.161313 at 20iterations 1.4097792E-03 0.2428741 at 30iterations 1.4078610E-04 1.9197464E-02 at 40iterations 1.3787877E-05 1.9452572E-03 at 50iterations finished qdiffx linear iterations at : 18:35:38 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.3787877E-05 1.9452572E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 18:35:39 4.477u 0.399s 0:05.16 94.1% 0+0k 0+0io 6pf+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 18:35:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.913053 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): -31.66800 17.37000 ymin,ymax (A): -22.96200 23.09900 zmin,zma (A): -11.96800 43.85900 x,y,z range (A): 49.03800 46.06100 55.82700 scale (grids/A): 1.913053 object centre (A): -7.149000 6.8499565E-02 15.94550 number of atom coordinates read : 2583 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 85.28380 86.84310 89.83564 assigned negative charge : -386.9045 centred at (gu) : 85.04527 87.04849 89.44614 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20930 grid for indexing accessible points = 1.400000 m= 26747 mr = 52860 m= 4116 mr = 20311 m= 229 mr = 2658 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2193 time to turn everything in is 0.5900000 number of dielectric boundary points 29654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19313 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) : 0.6376842 object centre at (A) : -7.149000 6.8499565E-02 15.94550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9126387E-02 2.3082806E-02 midg,1,midg; midg,igrid,midg 2.0157455E-02 -1.0279141E-03 1,midg,midg; igrid,midg,midg -1.7720072E-03 3.4908924E-02 gauss-seidel spectral radius is 0.9986371 estimated iterations to convergence 215 setup time was (sec) 0.8900000 now iterating at: 18:35:40 rms-change max change #iterations 4.208187 186.1281 at 10iterations 1.972566 64.94244 at 20iterations 0.9267908 30.95053 at 30iterations 0.4353576 15.10625 at 40iterations 0.2039360 6.231050 at 50iterations 9.5696397E-02 3.128574 at 60iterations 4.4860028E-02 1.426849 at 70iterations 2.0999813E-02 0.6853456 at 80iterations 9.8454123E-03 0.3230648 at 90iterations 4.6285391E-03 0.1500015 at 100iterations 2.1684673E-03 6.6558838E-02 at 110iterations 1.0176838E-03 3.6827087E-02 at 120iterations finished qdiffx linear iterations at : 18:35:49 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 1.0176838E-03 3.6827087E-02 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.45000 DelPhi exited at 18:35:50 10.457u 0.458s 0:11.43 95.3% 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 18:35:50 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.869579 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): -31.66800 17.37000 ymin,ymax (A): -22.96200 23.09900 zmin,zma (A): -11.96800 43.85900 x,y,z range (A): 49.03800 46.06100 55.82700 scale (grids/A): 2.869579 object centre (A): -7.149000 6.8499565E-02 15.94550 number of atom coordinates read : 2583 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 82.92566 85.26443 89.75336 assigned negative charge : -386.9045 centred at (gu) : 82.56782 85.57259 89.16920 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 172058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20930 grid for indexing accessible points = 1.400000 m= 87770 mr = 127223 m= 31071 mr = 73345 m= 7479 mr = 25545 m= 1123 mr = 5857 m= 77 mr = 797 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 7199 time to turn everything in is 1.560000 number of dielectric boundary points 66773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 19624 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) : 1.913053 object centre at (A) : -7.149000 6.8499565E-02 15.94550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7900199E-02 0.2050382 midg,1,midg; midg,igrid,midg 0.2136687 -8.8264914E-03 1,midg,midg; igrid,midg,midg 1.2954888E-02 0.4261462 gauss-seidel spectral radius is 0.9992525 estimated iterations to convergence 289 setup time was (sec) 1.890000 now iterating at: 18:35:52 rms-change max change #iterations 9.800735 403.7207 at 10iterations 5.647212 132.4724 at 20iterations 3.236813 61.68676 at 30iterations 1.855057 36.96995 at 40iterations 1.061542 19.92001 at 50iterations 0.6085263 11.16259 at 60iterations 0.3479882 6.640780 at 70iterations 0.1994528 3.795044 at 80iterations 0.1139912 2.094333 at 90iterations 6.5295041E-02 1.241512 at 100iterations 3.7399899E-02 0.7165184 at 110iterations 2.1384450E-02 0.3922272 at 120iterations 1.2244114E-02 0.2335911 at 130iterations 7.0079691E-03 0.1269512 at 140iterations 4.0136250E-03 7.6856136E-02 at 150iterations 2.2935460E-03 4.5509696E-02 at 160iterations 1.3153632E-03 2.4181366E-02 at 170iterations 7.5080589E-04 1.3599396E-02 at 180iterations finished qdiffx linear iterations at : 18:36:08 total time elapsed so far: 17.41000 # loops : 180 mean,max change (kT/e) : 7.5080589E-04 1.3599396E-02 energy calculations done at 17.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.57000 DelPhi exited at 18:36:08 17.577u 0.489s 0:18.32 98.5% 0+0k 0+0io 0pf+0w