Sun Oct 9 14:16:00 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 Sun Oct 9 2011 at 14:16:00 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5703391 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): 0.1880000 52.70400 ymin,ymax (A): -9.754000 39.84700 zmin,zma (A): -15.41100 47.00800 x,y,z range (A): 52.51600 49.60100 62.41900 scale (grids/A): 0.5703391 object centre (A): 26.44600 15.04650 15.79850 number of atom coordinates read : 2693 total number of charged atoms : 2547 net assigned charge : 6.445022 assigned positive charge : 409.9185 centred at (gu) : 89.56300 90.48482 88.42474 assigned negative charge : -403.4745 centred at (gu) : 89.51881 90.39294 88.47039 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5792 nv = 96 ne = 84 npr = 52706 no. pairs analyzed = 52706 no. exposed pairs = 3503 no. arc points = 24787 no. surface atoms = 1179 nbur = 1514 mkacc time = 0.1500000 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 = 1.512000 m= 267 mr = 2944 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2553 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7393 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3772113E-09 2.3365454E-10 midg,1,midg; midg,igrid,midg -3.0967368E-10 2.5699312E-09 1,midg,midg; igrid,midg,midg 3.7635386E-10 1.4582451E-09 gauss-seidel spectral radius is 0.9841180 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 14:16:01 rms-change max change #iterations 8.6802877E-02 15.02256 at 10iterations 6.4907563E-03 1.049043 at 20iterations 5.0128921E-04 8.9604855E-02 at 30iterations 4.6174198E-05 7.1296692E-03 at 40iterations 6.0725806E-06 9.3984604E-04 at 50iterations finished qdiffx linear iterations at : 14:16:05 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 6.0725806E-06 9.3984604E-04 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 14:16:05 4.075u 0.253s 0:04.76 90.7% 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 Sun Oct 9 2011 at 14:16:05 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.711017 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): 0.1880000 52.70400 ymin,ymax (A): -9.754000 39.84700 zmin,zma (A): -15.41100 47.00800 x,y,z range (A): 52.51600 49.60100 62.41900 scale (grids/A): 1.711017 object centre (A): 26.44600 15.04650 15.79850 number of atom coordinates read : 2693 total number of charged atoms : 2547 net assigned charge : 6.445022 assigned positive charge : 409.9185 centred at (gu) : 88.68835 91.45364 85.27367 assigned negative charge : -403.4745 centred at (gu) : 88.55618 91.17833 85.41084 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 63584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24787 grid for indexing accessible points = 1.400000 m= 20152 mr = 42447 m= 2319 mr = 13610 m= 70 mr = 1116 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 28948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19686 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) : 0.5703391 object centre at (A) : 26.44600 15.04650 15.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5647490E-02 9.8774778E-03 midg,1,midg; midg,igrid,midg -4.0654233E-04 3.8902222E-03 1,midg,midg; igrid,midg,midg -1.2346460E-02 -2.5623734E-03 gauss-seidel spectral radius is 0.9983307 estimated iterations to convergence 194 setup time was (sec) 0.8800000 now iterating at: 14:16:06 rms-change max change #iterations 3.490758 170.9721 at 10iterations 1.499477 76.52390 at 20iterations 0.6508426 24.52607 at 30iterations 0.2809614 10.13197 at 40iterations 0.1212636 5.005146 at 50iterations 5.2294172E-02 1.990856 at 60iterations 2.2627071E-02 0.8774261 at 70iterations 9.7693317E-03 0.3370118 at 80iterations 4.2366795E-03 0.1555753 at 90iterations 1.8328560E-03 6.3240051E-02 at 100iterations 7.9436781E-04 3.1110764E-02 at 110iterations 3.4396624E-04 1.3202667E-02 at 120iterations finished qdiffx linear iterations at : 14:16:15 total time elapsed so far: 9.050000 # loops : 120 mean,max change (kT/e) : 3.4396624E-04 1.3202667E-02 energy calculations done at 9.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.220000 DelPhi exited at 14:16:15 9.224u 0.286s 0:09.78 97.1% 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 Sun Oct 9 2011 at 14:16:15 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2693 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.566526 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): 0.1880000 52.70400 ymin,ymax (A): -9.754000 39.84700 zmin,zma (A): -15.41100 47.00800 x,y,z range (A): 52.51600 49.60100 62.41900 scale (grids/A): 2.566526 object centre (A): 26.44600 15.04650 15.79850 number of atom coordinates read : 2693 total number of charged atoms : 2547 net assigned charge : 6.445022 assigned positive charge : 409.9185 centred at (gu) : 88.03246 92.18034 82.91037 assigned negative charge : -403.4745 centred at (gu) : 87.83418 91.76756 83.11615 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 147693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24787 grid for indexing accessible points = 1.400000 m= 68630 mr = 104244 m= 20466 mr = 53579 m= 3585 mr = 15236 m= 319 mr = 2286 m= 8 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 65211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 20357 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) : 1.711017 object centre at (A) : 26.44600 15.04650 15.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9850642 0.1231624 midg,1,midg; midg,igrid,midg -2.0650499E-02 4.2002578E-03 1,midg,midg; igrid,midg,midg -0.1395403 -9.7609185E-02 gauss-seidel spectral radius is 0.9991786 estimated iterations to convergence 276 setup time was (sec) 1.740000 now iterating at: 14:16:17 rms-change max change #iterations 8.887568 311.3348 at 10iterations 5.111082 168.2328 at 20iterations 2.934942 71.26704 at 30iterations 1.667733 38.85043 at 40iterations 0.9435873 21.25584 at 50iterations 0.5324501 12.94518 at 60iterations 0.3001607 6.316858 at 70iterations 0.1681659 3.920223 at 80iterations 9.4529606E-02 1.874289 at 90iterations 5.2879289E-02 1.126831 at 100iterations 2.9628402E-02 0.7498093 at 110iterations 1.6571490E-02 0.3294525 at 120iterations 9.2782928E-03 0.1808167 at 130iterations 5.1777381E-03 0.1075859 at 140iterations 2.8983394E-03 5.9753418E-02 at 150iterations 1.6191939E-03 3.2569885E-02 at 160iterations 9.0682600E-04 1.9055843E-02 at 170iterations 5.0959160E-04 1.1494637E-02 at 180iterations finished qdiffx linear iterations at : 14:16:30 total time elapsed so far: 15.11000 # loops : 180 mean,max change (kT/e) : 5.0959160E-04 1.1494637E-02 energy calculations done at 15.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.29000 DelPhi exited at 14:16:31 15.292u 0.277s 0:15.84 98.2% 0+0k 0+0io 0pf+0w