Mon Oct 10 18:33:22 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 Mon Oct 10 2011 at 18:33:23 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6793764 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): 28.76700 74.71100 ymin,ymax (A): 98.54100 146.7990 zmin,zma (A): 31.33400 83.73500 x,y,z range (A): 45.94400 48.25800 52.40100 scale (grids/A): 0.6793764 object centre (A): 51.73900 122.6700 57.53450 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 1.028006 assigned positive charge : 361.1899 centred at (gu) : 89.09879 87.84952 89.32676 assigned negative charge : -360.1625 centred at (gu) : 89.01388 87.95979 89.30571 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7411 nv = 96 ne = 84 npr = 49793 no. pairs analyzed = 49793 no. exposed pairs = 2880 no. arc points = 19997 no. surface atoms = 971 nbur = 1431 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4244 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.3200000 number of dielectric boundary points 3533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1818 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7651743E-09 8.8029966E-09 midg,1,midg; midg,igrid,midg 5.6501733E-08 -1.8685908E-08 1,midg,midg; igrid,midg,midg -2.5947157E-08 2.3926336E-08 gauss-seidel spectral radius is 0.9887471 estimated iterations to convergence 77 setup time was (sec) 0.5600000 now iterating at: 18:33:23 rms-change max change #iterations 0.1862064 26.06370 at 10iterations 2.0974835E-02 2.689800 at 20iterations 2.5586579E-03 0.3730698 at 30iterations 3.8639701E-04 5.9871674E-02 at 40iterations 9.0121313E-05 1.4297485E-02 at 50iterations finished qdiffx linear iterations at : 18:33:26 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 9.0121313E-05 1.4297485E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 18:33:27 3.606u 0.212s 0:04.32 88.1% 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 Mon Oct 10 2011 at 18:33:27 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.038129 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): 28.76700 74.71100 ymin,ymax (A): 98.54100 146.7990 zmin,zma (A): 31.33400 83.73500 x,y,z range (A): 45.94400 48.25800 52.40100 scale (grids/A): 2.038129 object centre (A): 51.73900 122.6700 57.53450 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 1.028006 assigned positive charge : 361.1899 centred at (gu) : 87.29583 83.54812 87.97983 assigned negative charge : -360.1625 centred at (gu) : 87.04134 83.87912 87.91709 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 79081 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19997 grid for indexing accessible points = 1.400000 m= 31308 mr = 55958 m= 6026 mr = 23965 m= 418 mr = 4134 m= 7 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1453 time to turn everything in is 0.6200000 number of dielectric boundary points 32574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17950 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) : 0.6793764 object centre at (A) : 51.73900 122.6700 57.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3420604E-03 1.9830808E-02 midg,1,midg; midg,igrid,midg 3.1355809E-02 -9.4605321E-03 1,midg,midg; igrid,midg,midg -3.1170500E-03 1.3295060E-02 gauss-seidel spectral radius is 0.9987749 estimated iterations to convergence 226 setup time was (sec) 0.9600000 now iterating at: 18:33:28 rms-change max change #iterations 4.671659 212.2564 at 10iterations 2.270788 73.06654 at 20iterations 1.108258 35.15337 at 30iterations 0.5398779 16.35060 at 40iterations 0.2640869 7.887241 at 50iterations 0.1293496 4.239692 at 60iterations 6.3170947E-02 1.809608 at 70iterations 3.0839702E-02 0.8995171 at 80iterations 1.5073062E-02 0.4561272 at 90iterations 7.4183149E-03 0.2273235 at 100iterations 3.6578088E-03 0.1038551 at 110iterations 1.8418098E-03 5.1342010E-02 at 120iterations finished qdiffx linear iterations at : 18:33:35 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 1.8418098E-03 5.1342010E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 18:33:36 8.162u 0.239s 0:08.81 95.2% 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 Mon Oct 10 2011 at 18:33:36 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 3.057194 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): 28.76700 74.71100 ymin,ymax (A): 98.54100 146.7990 zmin,zma (A): 31.33400 83.73500 x,y,z range (A): 45.94400 48.25800 52.40100 scale (grids/A): 3.057194 object centre (A): 51.73900 122.6700 57.53450 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 1.028006 assigned positive charge : 361.1899 centred at (gu) : 85.94352 80.32195 86.96976 assigned negative charge : -360.1625 centred at (gu) : 85.56190 80.81857 86.87548 start vw surface at 0.2000000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 182530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19997 grid for indexing accessible points = 1.400000 m= 97296 mr = 134644 m= 40199 mr = 81372 m= 11221 mr = 33468 m= 1894 mr = 8881 m= 179 mr = 1404 m= 2 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 4720 time to turn everything in is 1.690000 number of dielectric boundary points 73452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 18116 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) : 2.038129 object centre at (A) : 51.73900 122.6700 57.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4137277 0.7819205 midg,1,midg; midg,igrid,midg 0.2278825 -9.0920404E-02 1,midg,midg; igrid,midg,midg 1.9812893E-02 4.0521156E-02 gauss-seidel spectral radius is 0.9992882 estimated iterations to convergence 296 setup time was (sec) 2.040000 now iterating at: 18:33:38 rms-change max change #iterations 10.54768 421.9694 at 10iterations 6.165631 131.3384 at 20iterations 3.600750 74.51678 at 30iterations 2.103861 38.71754 at 40iterations 1.223622 25.54248 at 50iterations 0.7123884 12.68498 at 60iterations 0.4153566 7.712412 at 70iterations 0.2414530 4.201469 at 80iterations 0.1403974 2.833454 at 90iterations 8.1648774E-02 1.474515 at 100iterations 4.7528725E-02 0.8130112 at 110iterations 2.7597137E-02 0.4540501 at 120iterations 1.6042955E-02 0.2807980 at 130iterations 9.3447240E-03 0.1658201 at 140iterations 5.4388964E-03 0.1100655 at 150iterations 3.1661550E-03 5.9918046E-02 at 160iterations 1.8607653E-03 3.1005859E-02 at 170iterations 1.1027538E-03 2.0643234E-02 at 180iterations finished qdiffx linear iterations at : 18:33:49 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 1.1027538E-03 2.0643234E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 18:33:50 13.348u 0.236s 0:13.86 97.9% 0+0k 0+0io 0pf+0w