Thu Jan 19 13:58:31 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 13:58:36 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5443 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ASP 553 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.1761661 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): 192.1630 276.3070 ymin,ymax (A): 63.18600 172.0420 zmin,zma (A): -67.16100 134.9210 x,y,z range (A): 84.14400 108.8560 202.0820 scale (grids/A): 0.1761661 object centre (A): 234.2350 117.6140 33.87999 number of atom coordinates read : 5443 total number of charged atoms : 5241 net assigned charge : -2.104952 assigned positive charge : 809.2096 centred at (gu) : 92.22571 86.87583 77.62016 assigned negative charge : -811.3217 centred at (gu) : 92.25773 86.87474 77.61581 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 594 nv = 96 ne = 84 npr = 109633 no. pairs analyzed = 109633 no. exposed pairs = 7312 no. arc points = 47512 no. surface atoms = 2484 nbur = 2959 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 4.966707 m= 5 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 457 no. dielectric boundary points in salt = 21 no. grid points charged and at boundary= 880 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 1057 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5516731E-25 5.8166610E-34 midg,1,midg; midg,igrid,midg -5.0151174E-29 -2.1203238E-31 1,midg,midg; igrid,midg,midg 9.4489418E-30 -2.7926788E-28 gauss-seidel spectral radius is 0.8510725 estimated iterations to convergence 23 setup time was (sec) 0.5700000 now iterating at: 13:58:39 rms-change max change #iterations 1.5180268E-04 0.1470714 at 10iterations 6.2217910E-06 6.3505173E-03 at 20iterations 3.0619913E-07 2.7418137E-04 at 30iterations 1.6560623E-08 1.6391277E-05 at 40iterations 3.6606813E-09 3.8146973E-06 at 50iterations finished qdiffx linear iterations at : 14:02:33 total time elapsed so far: 77.36000 # loops : 50 mean,max change (kT/e) : 3.6606813E-09 3.8146973E-06 energy calculations done at 77.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 77.48000 DelPhi exited at 14:02:37 77.471u 0.240s 4:02.52 32.0% 0+0k 0+0io 3pf+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 14:02:41 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5443 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ASP 553 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5284984 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): 192.1630 276.3070 ymin,ymax (A): 63.18600 172.0420 zmin,zma (A): -67.16100 134.9210 x,y,z range (A): 84.14400 108.8560 202.0820 scale (grids/A): 0.5284984 object centre (A): 234.2350 117.6140 33.87999 number of atom coordinates read : 5443 total number of charged atoms : 5241 net assigned charge : -2.104952 assigned positive charge : 809.2096 centred at (gu) : 96.67524 80.62566 52.85844 assigned negative charge : -811.3217 centred at (gu) : 96.77323 80.62399 52.84705 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47512 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 4.633574 m= 374 mr = 4723 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 5118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4592 ## 555 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 12548 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) : 0.1761661 object centre at (A) : 234.2350 117.6140 33.87999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9140387E-05 -2.0018367E-13 midg,1,midg; midg,igrid,midg -3.4661427E-09 1.2424436E-11 1,midg,midg; igrid,midg,midg 2.0671578E-10 -3.1853808E-09 gauss-seidel spectral radius is 0.9815701 estimated iterations to convergence 61 setup time was (sec) 0.4400000 now iterating at: 14:02:45 rms-change max change #iterations 7.8638740E-02 11.10182 at 10iterations 5.0921300E-03 0.7634850 at 20iterations 6.6303991E-04 0.1109810 at 30iterations 2.3209730E-04 4.2901993E-02 at 40iterations 9.1299844E-05 1.6803741E-02 at 50iterations 3.6231737E-05 6.5755844E-03 at 60iterations 1.4411630E-05 2.5749207E-03 at 70iterations 5.7370576E-06 1.0104179E-03 at 80iterations 2.2876363E-06 3.9768219E-04 at 90iterations 9.1537635E-07 1.5640259E-04 at 100iterations 3.7141811E-07 6.2942505E-05 at 110iterations 1.6115453E-07 2.6702881E-05 at 120iterations finished qdiffx linear iterations at : 14:03:40 total time elapsed so far: 18.40000 # loops : 120 mean,max change (kT/e) : 1.6115453E-07 2.6702881E-05 energy calculations done at 18.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.54000 DelPhi exited at 14:03:42 18.538u 0.196s 1:00.93 30.7% 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 Thu Jan 19 2012 at 14:03:47 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5443 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ASP 553 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.7927475 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): 192.1630 276.3070 ymin,ymax (A): 63.18600 172.0420 zmin,zma (A): -67.16100 134.9210 x,y,z range (A): 84.14400 108.8560 202.0820 scale (grids/A): 0.7927475 object centre (A): 234.2350 117.6140 33.87999 number of atom coordinates read : 5443 total number of charged atoms : 5241 net assigned charge : -2.104952 assigned positive charge : 809.2096 centred at (gu) : 100.0124 75.93790 34.28724 assigned negative charge : -811.3217 centred at (gu) : 100.1596 75.93591 34.27052 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 23726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47512 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 4.573004 m= 2316 mr = 13671 m= 26 mr = 652 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.3300000 number of dielectric boundary points 11745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3009 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 24059 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) : 0.5284984 object centre at (A) : 234.2350 117.6140 33.87999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1151784 -1.0452403E-10 midg,1,midg; midg,igrid,midg -1.8824094E-06 9.8442188E-09 1,midg,midg; igrid,midg,midg 1.0349615E-07 -1.7923504E-06 gauss-seidel spectral radius is 0.9916372 estimated iterations to convergence 89 setup time was (sec) 0.5500000 now iterating at: 14:03:51 rms-change max change #iterations 0.5765789 45.62890 at 10iterations 9.1913491E-02 8.669361 at 20iterations 1.4708220E-02 1.430973 at 30iterations 2.5276151E-03 0.2303820 at 40iterations 6.7458051E-04 5.9626579E-02 at 50iterations 3.1853881E-04 2.5759697E-02 at 60iterations 1.7472770E-04 1.3902664E-02 at 70iterations 9.7475640E-05 7.7686310E-03 at 80iterations 5.4576958E-05 4.3582916E-03 at 90iterations 3.0598305E-05 2.4623871E-03 at 100iterations 1.7166154E-05 1.3942719E-03 at 110iterations 9.6383455E-06 7.8964233E-04 at 120iterations 5.4157936E-06 4.5204163E-04 at 130iterations 3.0426024E-06 2.5749207E-04 at 140iterations 1.7203020E-06 1.4686584E-04 at 150iterations 9.8172075E-07 8.5830688E-05 at 160iterations 5.8172600E-07 5.4359436E-05 at 170iterations 3.6848928E-07 3.4332275E-05 at 180iterations finished qdiffx linear iterations at : 14:04:23 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 3.6848928E-07 3.4332275E-05 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 14:04:25 11.301u 0.205s 0:38.61 29.7% 0+0k 0+0io 0pf+0w