Sat Oct 15 15:10:38 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+sph2.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 = amb2.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 15 2011 at 15:10:38 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: HIR 76 has a net charge of 0.5140 !!! WARNING: SEP 238 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6451496 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): -5.062000 45.93300 ymin,ymax (A): 14.48800 65.47800 zmin,zma (A): -13.45300 41.72800 x,y,z range (A): 50.99500 50.99000 55.18100 scale (grids/A): 0.6451496 object centre (A): 20.43550 39.98300 14.13750 number of atom coordinates read : 2841 total number of charged atoms : 2686 net assigned charge : 3.679016 assigned positive charge : 431.4777 centred at (gu) : 90.20749 88.52662 89.13289 assigned negative charge : -427.7993 centred at (gu) : 90.02190 88.72395 89.19029 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7849 nv = 96 ne = 84 npr = 57232 no. pairs analyzed = 57232 no. exposed pairs = 3517 no. arc points = 24574 no. surface atoms = 1179 nbur = 1662 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 4375 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2468 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9556 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6873885E-08 -2.3519948E-09 midg,1,midg; midg,igrid,midg 4.6915442E-08 -1.7485403E-08 1,midg,midg; igrid,midg,midg -2.1314365E-08 3.3924728E-08 gauss-seidel spectral radius is 0.9875707 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 15:10:39 rms-change max change #iterations 0.1642343 23.88395 at 10iterations 1.6542850E-02 2.415284 at 20iterations 1.7482570E-03 0.2241883 at 30iterations 2.8378118E-04 4.1973114E-02 at 40iterations 9.3167189E-05 1.4783859E-02 at 50iterations finished qdiffx linear iterations at : 15:10:42 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 9.3167189E-05 1.4783859E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 15:10:43 3.952u 0.246s 0:04.47 93.7% 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 Sat Oct 15 2011 at 15:10:43 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: HIR 76 has a net charge of 0.5140 !!! WARNING: SEP 238 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.935449 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): -5.062000 45.93300 ymin,ymax (A): 14.48800 65.47800 zmin,zma (A): -13.45300 41.72800 x,y,z range (A): 50.99500 50.99000 55.18100 scale (grids/A): 1.935449 object centre (A): 20.43550 39.98300 14.13750 number of atom coordinates read : 2841 total number of charged atoms : 2686 net assigned charge : 3.679016 assigned positive charge : 431.4777 centred at (gu) : 90.62191 85.57930 87.39827 assigned negative charge : -427.7993 centred at (gu) : 90.06549 86.17147 87.57067 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 83579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24574 grid for indexing accessible points = 1.400000 m= 32689 mr = 58158 m= 5626 mr = 24346 m= 336 mr = 3530 m= 3 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 151 time to turn everything in is 0.4500000 number of dielectric boundary points 36091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 21174 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) : 0.6451496 object centre at (A) : 20.43550 39.98300 14.13750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9762605E-02 -8.8379458E-03 midg,1,midg; midg,igrid,midg 0.1121829 -2.0182475E-02 1,midg,midg; igrid,midg,midg -4.4930987E-02 6.7028008E-02 gauss-seidel spectral radius is 0.9987016 estimated iterations to convergence 220 setup time was (sec) 0.7300000 now iterating at: 15:10:44 rms-change max change #iterations 4.648815 228.3706 at 10iterations 2.239168 74.26646 at 20iterations 1.072051 35.28241 at 30iterations 0.5135572 15.14095 at 40iterations 0.2463220 7.802777 at 50iterations 0.1181021 3.622704 at 60iterations 5.6596208E-02 1.681406 at 70iterations 2.7131770E-02 0.8328857 at 80iterations 1.2987200E-02 0.3722992 at 90iterations 6.2694428E-03 0.2012424 at 100iterations 3.0282240E-03 9.0255737E-02 at 110iterations 1.4918555E-03 4.5477867E-02 at 120iterations finished qdiffx linear iterations at : 15:10:52 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 1.4918555E-03 4.5477867E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 15:10:53 9.328u 0.281s 0:10.15 94.5% 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 15 2011 at 15:10:53 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: HIR 76 has a net charge of 0.5140 !!! WARNING: SEP 238 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.903173 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): -5.062000 45.93300 ymin,ymax (A): 14.48800 65.47800 zmin,zma (A): -13.45300 41.72800 x,y,z range (A): 50.99500 50.99000 55.18100 scale (grids/A): 2.903173 object centre (A): 20.43550 39.98300 14.13750 number of atom coordinates read : 2841 total number of charged atoms : 2686 net assigned charge : 3.679016 assigned positive charge : 431.4777 centred at (gu) : 90.93262 83.36882 86.09730 assigned negative charge : -427.7993 centred at (gu) : 90.09824 84.25732 86.35598 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 192794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24574 grid for indexing accessible points = 1.400000 m= 102790 mr = 140459 m= 40269 mr = 84624 m= 10336 mr = 32557 m= 1456 mr = 7700 m= 83 mr = 878 m= 0 mr = 30 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 488 time to turn everything in is 1.180000 number of dielectric boundary points 81480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 21484 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) : 1.935449 object centre at (A) : 20.43550 39.98300 14.13750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.006897 5.6245584E-02 midg,1,midg; midg,igrid,midg 1.157664 -0.1055791 1,midg,midg; igrid,midg,midg -0.6538752 0.7673786 gauss-seidel spectral radius is 0.9992822 estimated iterations to convergence 295 setup time was (sec) 1.480000 now iterating at: 15:10:55 rms-change max change #iterations 10.81116 328.8669 at 10iterations 6.385209 135.6077 at 20iterations 3.750322 69.40824 at 30iterations 2.198173 38.91625 at 40iterations 1.283739 24.25953 at 50iterations 0.7500303 13.16107 at 60iterations 0.4373497 8.052759 at 70iterations 0.2547841 4.325727 at 80iterations 0.1481454 2.595604 at 90iterations 8.6169541E-02 1.442131 at 100iterations 5.0087173E-02 0.8972247 at 110iterations 2.9036321E-02 0.5444183 at 120iterations 1.6912377E-02 0.3002281 at 130iterations 9.8190391E-03 0.1682301 at 140iterations 5.7140961E-03 9.4917297E-02 at 150iterations 3.3338347E-03 5.9787750E-02 at 160iterations 1.9558403E-03 3.3756256E-02 at 170iterations 1.1667502E-03 2.1356583E-02 at 180iterations finished qdiffx linear iterations at : 15:11:09 total time elapsed so far: 15.40000 # loops : 180 mean,max change (kT/e) : 1.1667502E-03 2.1356583E-02 energy calculations done at 15.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.53000 DelPhi exited at 15:11:09 15.528u 0.348s 0:16.26 97.5% 0+0k 0+0io 0pf+0w