Thu Jan 19 13:32:12 PST 2012 #!/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 Thu Jan 19 2012 at 13:32:16 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4239357 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): -10.68700 73.28800 ymin,ymax (A): -56.08100 11.58800 zmin,zma (A): -102.3920 -22.85100 x,y,z range (A): 83.97501 67.66900 79.54100 scale (grids/A): 0.4239357 object centre (A): 31.30050 -22.24650 -62.62150 number of atom coordinates read : 6831 total number of charged atoms : 6661 net assigned charge : 1.200043 assigned positive charge : 1045.192 centred at (gu) : 88.25111 89.61608 89.79559 assigned negative charge : -1044.000 centred at (gu) : 88.17155 89.53536 89.73629 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7532 nv = 96 ne = 84 npr = 131507 no. pairs analyzed = 131507 no. exposed pairs = 9525 no. arc points = 65353 no. surface atoms = 3148 nbur = 3683 mkacc time = 0.2300000 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 = 1.960000 m= 198 mr = 3381 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5375 ## 1174 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10409 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5117547E-12 2.6400626E-12 midg,1,midg; midg,igrid,midg -3.7392966E-12 3.3034985E-12 1,midg,midg; igrid,midg,midg -5.7162838E-12 2.1265587E-12 gauss-seidel spectral radius is 0.9717934 estimated iterations to convergence 50 setup time was (sec) 0.6200000 now iterating at: 13:32:20 rms-change max change #iterations 2.7755512E-02 4.993561 at 10iterations 1.2497408E-03 0.1981049 at 20iterations 3.1645247E-04 3.9127350E-02 at 30iterations 1.1669091E-04 1.4741898E-02 at 40iterations 4.3594271E-05 5.6533813E-03 at 50iterations finished qdiffx linear iterations at : 13:32:29 total time elapsed so far: 3.710000 # loops : 50 mean,max change (kT/e) : 4.3594271E-05 5.6533813E-03 energy calculations done at 3.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 13:32:30 3.841u 0.189s 0:15.11 26.6% 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 Thu Jan 19 2012 at 13:32:34 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.271807 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): -10.68700 73.28800 ymin,ymax (A): -56.08100 11.58800 zmin,zma (A): -102.3920 -22.85100 x,y,z range (A): 83.97501 67.66900 79.54100 scale (grids/A): 1.271807 object centre (A): 31.30050 -22.24650 -62.62150 number of atom coordinates read : 6831 total number of charged atoms : 6661 net assigned charge : 1.200043 assigned positive charge : 1045.192 centred at (gu) : 84.75134 88.84681 89.38505 assigned negative charge : -1044.000 centred at (gu) : 84.51417 88.60558 89.20821 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 88382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 65353 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 21307 mr = 57005 m= 1000 mr = 12493 m= 7 mr = 186 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 210 time to turn everything in is 0.4900000 number of dielectric boundary points 41012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1276 ## 62 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 45731 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) : 0.4239357 object centre at (A) : 31.30050 -22.24650 -62.62150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8713995E-03 4.3330635E-03 midg,1,midg; midg,igrid,midg -2.7940818E-03 2.1401723E-03 1,midg,midg; igrid,midg,midg -1.1848702E-02 1.6633985E-03 gauss-seidel spectral radius is 0.9973489 estimated iterations to convergence 155 setup time was (sec) 0.7100000 now iterating at: 13:32:39 rms-change max change #iterations 2.973862 129.3656 at 10iterations 1.030709 41.76322 at 20iterations 0.3572533 13.35328 at 30iterations 0.1244949 4.854317 at 40iterations 4.3242637E-02 1.538311 at 50iterations 1.5151011E-02 0.5519629 at 60iterations 5.3205728E-03 0.2062787 at 70iterations 1.9242058E-03 6.7530632E-02 at 80iterations 7.5713819E-04 2.5967598E-02 at 90iterations 3.6035947E-04 1.2847900E-02 at 100iterations 2.1211115E-04 7.0877075E-03 at 110iterations 1.4006703E-04 4.0035248E-03 at 120iterations finished qdiffx linear iterations at : 13:33:03 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 1.4006703E-04 4.0035248E-03 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 13:33:04 8.292u 0.216s 0:29.91 28.4% 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 Thu Jan 19 2012 at 13:33:06 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.907710 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): -10.68700 73.28800 ymin,ymax (A): -56.08100 11.58800 zmin,zma (A): -102.3920 -22.85100 x,y,z range (A): 83.97501 67.66900 79.54100 scale (grids/A): 1.907710 object centre (A): 31.30050 -22.24650 -62.62150 number of atom coordinates read : 6831 total number of charged atoms : 6661 net assigned charge : 1.200043 assigned positive charge : 1045.192 centred at (gu) : 82.12638 88.26972 89.07690 assigned negative charge : -1044.000 centred at (gu) : 81.77111 87.90821 88.81229 start vw surface at 0.1700000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 206722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 65353 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 82662 mr = 142585 m= 14620 mr = 60252 m= 921 mr = 9148 m= 7 mr = 311 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 799 time to turn everything in is 1.080000 number of dielectric boundary points 92636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 377 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 52477 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) : 1.271807 object centre at (A) : 31.30050 -22.24650 -62.62150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1365776 0.1002788 midg,1,midg; midg,igrid,midg -6.8627924E-02 5.9030365E-02 1,midg,midg; igrid,midg,midg -0.4359286 8.3252504E-02 gauss-seidel spectral radius is 0.9989743 estimated iterations to convergence 247 setup time was (sec) 1.350000 now iterating at: 13:33:13 rms-change max change #iterations 9.382294 330.8896 at 10iterations 5.106739 132.1835 at 20iterations 2.747653 68.60517 at 30iterations 1.466782 39.52115 at 40iterations 0.7790322 23.95459 at 50iterations 0.4122219 12.44678 at 60iterations 0.2171398 5.270868 at 70iterations 0.1142324 2.513931 at 80iterations 6.0009763E-02 1.397175 at 90iterations 3.1472828E-02 0.7078362 at 100iterations 1.6498366E-02 0.3441048 at 110iterations 8.6097410E-03 0.1841145 at 120iterations 4.5012399E-03 9.9205017E-02 at 130iterations 2.3553497E-03 5.3964615E-02 at 140iterations 1.2287465E-03 2.7022004E-02 at 150iterations 6.4155046E-04 1.3668060E-02 at 160iterations 3.3531256E-04 7.3852539E-03 at 170iterations 1.7501922E-04 3.5822392E-03 at 180iterations finished qdiffx linear iterations at : 13:33:43 total time elapsed so far: 13.68000 # loops : 180 mean,max change (kT/e) : 1.7501922E-04 3.5822392E-03 energy calculations done at 13.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.81000 DelPhi exited at 13:33:43 13.813u 0.237s 0:37.61 37.3% 0+0k 0+0io 0pf+0w