Sun Oct 9 22:19:21 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 22:19:22 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN1 1551 has a net charge of 1.4000 !!! WARNING: ZN1 1555 has a net charge of 1.4000 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: 0.6638200 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): 16.77900 70.29600 ymin,ymax (A): -38.00600 15.62300 zmin,zma (A): -8.650000 43.81700 x,y,z range (A): 53.51700 53.62900 52.46700 scale (grids/A): 0.6638200 object centre (A): 43.53750 -11.19150 17.58350 number of atom coordinates read : 3133 total number of charged atoms : 2983 net assigned charge : 6.425009 assigned positive charge : 477.9438 centred at (gu) : 90.59718 88.55056 90.63956 assigned negative charge : -471.5201 centred at (gu) : 90.48404 88.48336 90.62303 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 9342 nv = 96 ne = 84 npr = 61868 no. pairs analyzed = 61868 no. exposed pairs = 4010 no. arc points = 28664 no. surface atoms = 1348 nbur = 1785 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 532 mr = 5030 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2300000 number of dielectric boundary points 4791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2771 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 11043 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2143644E-08 2.5601219E-08 midg,1,midg; midg,igrid,midg -9.0480845E-11 2.6626585E-08 1,midg,midg; igrid,midg,midg -1.0575492E-08 5.3958360E-08 gauss-seidel spectral radius is 0.9882931 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 22:19:22 rms-change max change #iterations 0.1933031 25.61303 at 10iterations 2.0631952E-02 2.755739 at 20iterations 2.2466460E-03 0.2758293 at 30iterations 2.4198797E-04 3.4946442E-02 at 40iterations 2.7660966E-05 3.3564568E-03 at 50iterations finished qdiffx linear iterations at : 22:19:25 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.7660966E-05 3.3564568E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 22:19:25 3.430u 0.192s 0:03.96 91.4% 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 Sun Oct 9 2011 at 22:19:26 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN1 1551 has a net charge of 1.4000 !!! WARNING: ZN1 1555 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.991460 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): 16.77900 70.29600 ymin,ymax (A): -38.00600 15.62300 zmin,zma (A): -8.650000 43.81700 x,y,z range (A): 53.51700 53.62900 52.46700 scale (grids/A): 1.991460 object centre (A): 43.53750 -11.19150 17.58350 number of atom coordinates read : 3133 total number of charged atoms : 2983 net assigned charge : 6.425009 assigned positive charge : 477.9438 centred at (gu) : 91.79086 85.65144 91.91818 assigned negative charge : -471.5201 centred at (gu) : 91.45181 85.44982 91.86885 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 100660 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28664 grid for indexing accessible points = 1.400000 m= 36685 mr = 69057 m= 6277 mr = 26974 m= 438 mr = 3911 m= 3 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2124 time to turn everything in is 0.4800000 number of dielectric boundary points 43931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 23535 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) : 0.6638200 object centre at (A) : 43.53750 -11.19150 17.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9228608E-03 -2.0703733E-02 midg,1,midg; midg,igrid,midg 8.2052365E-02 4.8360568E-02 1,midg,midg; igrid,midg,midg 1.8596383E-03 3.9549168E-02 gauss-seidel spectral radius is 0.9988038 estimated iterations to convergence 229 setup time was (sec) 0.7000000 now iterating at: 22:19:26 rms-change max change #iterations 5.171065 201.1576 at 10iterations 2.544482 84.01054 at 20iterations 1.244720 32.87053 at 30iterations 0.6103714 18.35521 at 40iterations 0.2997193 8.470396 at 50iterations 0.1472974 3.991776 at 60iterations 7.2321884E-02 2.081783 at 70iterations 3.5501774E-02 0.9418035 at 80iterations 1.7471747E-02 0.5230904 at 90iterations 8.5651567E-03 0.2401443 at 100iterations 4.2060730E-03 0.1116982 at 110iterations 2.0753571E-03 5.9486389E-02 at 120iterations finished qdiffx linear iterations at : 22:19:34 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 2.0753571E-03 5.9486389E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 22:19:34 8.099u 0.208s 0:08.73 94.9% 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 22:19:34 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN1 1551 has a net charge of 1.4000 !!! WARNING: ZN1 1555 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.987190 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): 16.77900 70.29600 ymin,ymax (A): -38.00600 15.62300 zmin,zma (A): -8.650000 43.81700 x,y,z range (A): 53.51700 53.62900 52.46700 scale (grids/A): 2.987190 object centre (A): 43.53750 -11.19150 17.58350 number of atom coordinates read : 3133 total number of charged atoms : 2983 net assigned charge : 6.425009 assigned positive charge : 477.9438 centred at (gu) : 92.68616 83.47684 92.87709 assigned negative charge : -471.5201 centred at (gu) : 92.17765 83.17446 92.80318 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 232658 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28664 grid for indexing accessible points = 1.400000 m= 117347 mr = 167733 m= 43596 mr = 95460 m= 11331 mr = 34704 m= 1901 mr = 8512 m= 155 mr = 1396 m= 5 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 6872 time to turn everything in is 1.280000 number of dielectric boundary points 99095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 23864 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) : 1.991460 object centre at (A) : 43.53750 -11.19150 17.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7457608E-02 -0.3756605 midg,1,midg; midg,igrid,midg 0.6067893 0.3931062 1,midg,midg; igrid,midg,midg 0.2223893 0.4883617 gauss-seidel spectral radius is 0.9993219 estimated iterations to convergence 303 setup time was (sec) 1.520000 now iterating at: 22:19:36 rms-change max change #iterations 11.99296 436.2034 at 10iterations 7.221124 159.0558 at 20iterations 4.320761 81.91655 at 30iterations 2.587228 58.61721 at 40iterations 1.538640 27.81184 at 50iterations 0.9158039 17.46924 at 60iterations 0.5429283 10.66056 at 70iterations 0.3220605 5.746748 at 80iterations 0.1904272 2.977065 at 90iterations 0.1127870 1.855564 at 100iterations 6.6607915E-02 1.055988 at 110iterations 3.9331287E-02 0.6193314 at 120iterations 2.3254484E-02 0.3982849 at 130iterations 1.3689467E-02 0.2540398 at 140iterations 8.0849044E-03 0.1344914 at 150iterations 4.7652628E-03 8.1081033E-02 at 160iterations 2.8072463E-03 4.3554306E-02 at 170iterations 1.6594181E-03 2.6109695E-02 at 180iterations finished qdiffx linear iterations at : 22:19:48 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 1.6594181E-03 2.6109695E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 22:19:48 13.577u 0.221s 0:14.06 98.0% 0+0k 0+0io 0pf+0w