Tue Oct 11 03:49:18 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 Tue Oct 11 2011 at 03:49:18 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 = 2673 !!! WARNING: HIR 69 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6740126 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): -9.417000 36.74600 ymin,ymax (A): -27.43400 21.68500 zmin,zma (A): -7.296000 45.52200 x,y,z range (A): 46.16300 49.11900 52.81800 scale (grids/A): 0.6740126 object centre (A): 13.66450 -2.874500 19.11300 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 4.514014 assigned positive charge : 407.2859 centred at (gu) : 89.53989 90.36355 91.33156 assigned negative charge : -402.7723 centred at (gu) : 89.26532 90.19125 91.30971 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8136 nv = 96 ne = 84 npr = 55053 no. pairs analyzed = 55053 no. exposed pairs = 3223 no. arc points = 22209 no. surface atoms = 1087 nbur = 1586 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 485 mr = 4696 m= 5 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3800000 number of dielectric boundary points 3860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9432 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1786231E-09 3.0396961E-08 midg,1,midg; midg,igrid,midg -3.1644792E-08 7.1324735E-08 1,midg,midg; igrid,midg,midg -7.2139258E-08 8.6078806E-08 gauss-seidel spectral radius is 0.9885905 estimated iterations to convergence 76 setup time was (sec) 0.6600000 now iterating at: 03:49:19 rms-change max change #iterations 0.1887112 27.82756 at 10iterations 2.1232853E-02 2.680061 at 20iterations 2.4371115E-03 0.2989655 at 30iterations 3.0414184E-04 3.8415909E-02 at 40iterations 4.8120502E-05 6.6184998E-03 at 50iterations finished qdiffx linear iterations at : 03:49:22 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 4.8120502E-05 6.6184998E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 03:49:23 4.078u 0.173s 0:04.56 92.9% 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 Tue Oct 11 2011 at 03:49:23 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 !!! WARNING: HIR 69 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: 2.022038 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): -9.417000 36.74600 ymin,ymax (A): -27.43400 21.68500 zmin,zma (A): -7.296000 45.52200 x,y,z range (A): 46.16300 49.11900 52.81800 scale (grids/A): 2.022038 object centre (A): 13.66450 -2.874500 19.11300 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 4.514014 assigned positive charge : 407.2859 centred at (gu) : 88.61936 91.09025 93.99418 assigned negative charge : -402.7723 centred at (gu) : 87.79588 90.57351 93.92879 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 87374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22209 grid for indexing accessible points = 1.400000 m= 33808 mr = 62363 m= 5899 mr = 25783 m= 417 mr = 3972 m= 5 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 271 time to turn everything in is 0.8200000 number of dielectric boundary points 35208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19989 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) : 0.6740126 object centre at (A) : 13.66450 -2.874500 19.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2671420E-02 7.2099129E-03 midg,1,midg; midg,igrid,midg -1.1944235E-02 5.2229933E-02 1,midg,midg; igrid,midg,midg -3.6326803E-02 7.2831556E-02 gauss-seidel spectral radius is 0.9987851 estimated iterations to convergence 227 setup time was (sec) 1.180000 now iterating at: 03:49:24 rms-change max change #iterations 4.908517 195.4151 at 10iterations 2.405505 77.94749 at 20iterations 1.179085 36.89245 at 30iterations 0.5775803 17.02591 at 40iterations 0.2834344 8.404812 at 50iterations 0.1389358 4.055252 at 60iterations 6.7854941E-02 1.806579 at 70iterations 3.3365946E-02 1.075605 at 80iterations 1.6338773E-02 0.4791832 at 90iterations 8.0116615E-03 0.2233810 at 100iterations 3.9319103E-03 0.1060686 at 110iterations 1.9325829E-03 5.7149887E-02 at 120iterations finished qdiffx linear iterations at : 03:49:33 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 1.9325829E-03 5.7149887E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 03:49:33 9.722u 0.266s 0:10.40 95.9% 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 Tue Oct 11 2011 at 03:49:33 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 = 2673 !!! WARNING: HIR 69 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.033057 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): -9.417000 36.74600 ymin,ymax (A): -27.43400 21.68500 zmin,zma (A): -7.296000 45.52200 x,y,z range (A): 46.16300 49.11900 52.81800 scale (grids/A): 3.033057 object centre (A): 13.66450 -2.874500 19.11300 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 4.514014 assigned positive charge : 407.2859 centred at (gu) : 87.92886 91.63517 95.99120 assigned negative charge : -402.7723 centred at (gu) : 86.69371 90.86040 95.89306 start vw surface at 0.2100000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 201625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22209 grid for indexing accessible points = 1.400000 m= 107343 mr = 150145 m= 41735 mr = 89616 m= 10893 mr = 34520 m= 1814 mr = 8521 m= 125 mr = 1297 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 856 time to turn everything in is 2.190000 number of dielectric boundary points 79383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.360000 number of grid points assigned charge 20206 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) : 2.022038 object centre at (A) : 13.66450 -2.874500 19.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8800124E-02 0.2659703 midg,1,midg; midg,igrid,midg -0.1218755 0.5418351 1,midg,midg; igrid,midg,midg -0.2809509 0.6008841 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 2.570000 now iterating at: 03:49:36 rms-change max change #iterations 11.11000 352.7659 at 10iterations 6.562724 134.8626 at 20iterations 3.850175 89.88641 at 30iterations 2.260621 44.86813 at 40iterations 1.326967 20.98355 at 50iterations 0.7771735 14.56568 at 60iterations 0.4545273 7.822674 at 70iterations 0.2656916 4.415382 at 80iterations 0.1554520 2.447734 at 90iterations 9.0771161E-02 1.551383 at 100iterations 5.2995484E-02 0.9348297 at 110iterations 3.1022271E-02 0.5368938 at 120iterations 1.8122464E-02 0.3020859 at 130iterations 1.0660880E-02 0.1942849 at 140iterations 6.2608160E-03 9.7983599E-02 at 150iterations 3.7073428E-03 6.4682007E-02 at 160iterations 2.2305907E-03 3.6819458E-02 at 170iterations 1.3658672E-03 2.6468277E-02 at 180iterations finished qdiffx linear iterations at : 03:49:49 total time elapsed so far: 15.64000 # loops : 180 mean,max change (kT/e) : 1.3658672E-03 2.6468277E-02 energy calculations done at 15.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 03:49:50 15.866u 0.314s 0:16.63 97.2% 0+0k 0+0io 0pf+0w