Tue Oct 11 06:19:03 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 06:19:03 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 = 2056 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: 0.7248590 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): 18.11300 64.38500 ymin,ymax (A): -3.534000 33.21400 zmin,zma (A): 21.12100 70.23400 x,y,z range (A): 46.27200 36.74800 49.11300 scale (grids/A): 0.7248590 object centre (A): 41.24900 14.84000 45.67750 number of atom coordinates read : 2056 total number of charged atoms : 1927 net assigned charge : 6.500006 assigned positive charge : 311.3940 centred at (gu) : 90.05157 89.70331 89.24433 assigned negative charge : -304.8942 centred at (gu) : 90.20631 89.76829 89.24602 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7332 nv = 96 ne = 84 npr = 41247 no. pairs analyzed = 41247 no. exposed pairs = 2409 no. arc points = 16713 no. surface atoms = 820 nbur = 1236 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 508 mr = 4272 m= 4 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1556 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5613430E-08 7.0367072E-08 midg,1,midg; midg,igrid,midg 1.3488413E-07 3.4061625E-08 1,midg,midg; igrid,midg,midg 1.8773208E-07 -2.9290840E-08 gauss-seidel spectral radius is 0.9900702 estimated iterations to convergence 82 setup time was (sec) 0.4700000 now iterating at: 06:19:03 rms-change max change #iterations 0.2189066 34.51326 at 10iterations 2.8235393E-02 4.628848 at 20iterations 3.8546051E-03 0.5324020 at 30iterations 5.8464077E-04 8.0047607E-02 at 40iterations 1.2444337E-04 1.8310547E-02 at 50iterations finished qdiffx linear iterations at : 06:19:06 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 1.2444337E-04 1.8310547E-02 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 06:19:07 3.210u 0.174s 0:03.92 86.2% 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 Tue Oct 11 2011 at 06:19:07 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 = 2056 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: 2.174577 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): 18.11300 64.38500 ymin,ymax (A): -3.534000 33.21400 zmin,zma (A): 21.12100 70.23400 x,y,z range (A): 46.27200 36.74800 49.11300 scale (grids/A): 2.174577 object centre (A): 41.24900 14.84000 45.67750 number of atom coordinates read : 2056 total number of charged atoms : 1927 net assigned charge : 6.500006 assigned positive charge : 311.3940 centred at (gu) : 90.15479 89.10998 87.73304 assigned negative charge : -304.8942 centred at (gu) : 90.61915 89.30498 87.73822 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16713 grid for indexing accessible points = 1.400000 m= 32158 mr = 56119 m= 6733 mr = 24938 m= 726 mr = 4621 m= 22 mr = 439 m= 0 mr = 4 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 31610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15332 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) : 0.7248590 object centre at (A) : 41.24900 14.84000 45.67750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5505615E-02 6.3778624E-02 midg,1,midg; midg,igrid,midg 3.6178581E-02 1.1990143E-03 1,midg,midg; igrid,midg,midg 4.8153434E-02 2.7320502E-02 gauss-seidel spectral radius is 0.9988745 estimated iterations to convergence 236 setup time was (sec) 0.8600000 now iterating at: 06:19:08 rms-change max change #iterations 4.748284 175.5779 at 10iterations 2.378015 83.09724 at 20iterations 1.204873 39.36645 at 30iterations 0.6056997 17.71139 at 40iterations 0.3045153 9.134020 at 50iterations 0.1541061 4.619744 at 60iterations 7.7267148E-02 2.222237 at 70iterations 3.9011650E-02 1.248772 at 80iterations 1.9641161E-02 0.5896873 at 90iterations 9.9182148E-03 0.2684879 at 100iterations 5.0173462E-03 0.1638572 at 110iterations 2.5525100E-03 7.4960709E-02 at 120iterations finished qdiffx linear iterations at : 06:19:14 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 2.5525100E-03 7.4960709E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 06:19:15 7.430u 0.213s 0:07.95 96.1% 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 06:19:15 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 = 2056 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: 3.261866 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): 18.11300 64.38500 ymin,ymax (A): -3.534000 33.21400 zmin,zma (A): 21.12100 70.23400 x,y,z range (A): 46.27200 36.74800 49.11300 scale (grids/A): 3.261866 object centre (A): 41.24900 14.84000 45.67750 number of atom coordinates read : 2056 total number of charged atoms : 1927 net assigned charge : 6.500006 assigned positive charge : 311.3940 centred at (gu) : 90.23215 88.66506 86.59953 assigned negative charge : -304.8942 centred at (gu) : 90.92880 88.95749 86.60731 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 179558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16713 grid for indexing accessible points = 1.400000 m= 99448 mr = 134630 m= 41981 mr = 83634 m= 12932 mr = 34990 m= 2842 mr = 10220 m= 386 mr = 2159 m= 9 mr = 280 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 71243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 15416 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) : 2.174577 object centre at (A) : 41.24900 14.84000 45.67750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2117288 0.5422682 midg,1,midg; midg,igrid,midg 0.2841184 1.3311443E-02 1,midg,midg; igrid,midg,midg 0.3606298 0.4313751 gauss-seidel spectral radius is 0.9993039 estimated iterations to convergence 299 setup time was (sec) 2.100000 now iterating at: 06:19:17 rms-change max change #iterations 10.45152 405.4949 at 10iterations 6.197021 132.9554 at 20iterations 3.669823 71.68860 at 30iterations 2.176196 45.14250 at 40iterations 1.284169 22.29979 at 50iterations 0.7556930 13.49466 at 60iterations 0.4460946 8.567083 at 70iterations 0.2624600 4.715301 at 80iterations 0.1542895 2.584845 at 90iterations 9.0797208E-02 1.514275 at 100iterations 5.3545818E-02 0.9861603 at 110iterations 3.1468563E-02 0.5363197 at 120iterations 1.8699944E-02 0.3553085 at 130iterations 1.1162765E-02 0.2101693 at 140iterations 6.7933858E-03 0.1115150 at 150iterations 4.2608907E-03 7.8025818E-02 at 160iterations 2.7842042E-03 5.3058624E-02 at 170iterations 1.9299351E-03 3.8002014E-02 at 180iterations finished qdiffx linear iterations at : 06:19:27 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 1.9299351E-03 3.8002014E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 06:19:28 12.496u 0.213s 0:13.35 95.1% 0+0k 0+0io 0pf+0w