Sat Oct 15 14:22:54 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 Sat Oct 15 2011 at 14:22:54 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6428894 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 0.6428894 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 530.7694 centred at (gu) : 89.39759 90.86659 89.24841 assigned negative charge : -527.7706 centred at (gu) : 89.42230 90.82481 89.31862 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9402 nv = 96 ne = 84 npr = 71539 no. pairs analyzed = 71539 no. exposed pairs = 3869 no. arc points = 26577 no. surface atoms = 1301 nbur = 2150 mkacc time = 0.2400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 5564 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.5100000 number of dielectric boundary points 4290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 11447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9372770E-08 -6.4072090E-09 midg,1,midg; midg,igrid,midg -2.1571465E-09 1.4044132E-08 1,midg,midg; igrid,midg,midg 9.9588213E-09 2.8906860E-10 gauss-seidel spectral radius is 0.9875273 estimated iterations to convergence 73 setup time was (sec) 0.8800000 now iterating at: 14:22:55 rms-change max change #iterations 0.1760499 22.23739 at 10iterations 1.8232660E-02 2.232074 at 20iterations 2.1502057E-03 0.2509880 at 30iterations 5.5744633E-04 8.3499908E-02 at 40iterations 2.4985441E-04 3.6420822E-02 at 50iterations finished qdiffx linear iterations at : 14:22:59 total time elapsed so far: 4.950000 # loops : 50 mean,max change (kT/e) : 2.4985441E-04 3.6420822E-02 energy calculations done at 4.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.170000 DelPhi exited at 14:23:00 5.176u 0.426s 0:05.96 93.7% 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 Sat Oct 15 2011 at 14:23:00 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.928668 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 1.928668 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 530.7694 centred at (gu) : 88.19186 92.59868 87.74445 assigned negative charge : -527.7706 centred at (gu) : 88.26646 92.47413 87.95547 start vw surface at 0.1800000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 101550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26577 grid for indexing accessible points = 1.400000 m= 39865 mr = 74079 m= 6821 mr = 30454 m= 442 mr = 4368 m= 8 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 1854 time to turn everything in is 1.040000 number of dielectric boundary points 39629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 26067 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) : 0.6428894 object centre at (A) : 37.49150 -15.45050 58.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9478973E-02 -5.7278797E-03 midg,1,midg; midg,igrid,midg -7.3706778E-03 2.9082265E-02 1,midg,midg; igrid,midg,midg 1.5725417E-02 4.3347411E-02 gauss-seidel spectral radius is 0.9987346 estimated iterations to convergence 223 setup time was (sec) 1.420000 now iterating at: 14:23:02 rms-change max change #iterations 5.185490 207.6122 at 10iterations 2.507549 67.43738 at 20iterations 1.217041 33.09141 at 30iterations 0.5877945 16.78393 at 40iterations 0.2846603 8.295963 at 50iterations 0.1376798 3.716248 at 60iterations 6.6724904E-02 2.078667 at 70iterations 3.2340698E-02 0.9459724 at 80iterations 1.5724035E-02 0.4224472 at 90iterations 7.7108545E-03 0.2374802 at 100iterations 3.8372143E-03 0.1190453 at 110iterations 1.9920906E-03 5.1322937E-02 at 120iterations finished qdiffx linear iterations at : 14:23:13 total time elapsed so far: 12.29000 # loops : 120 mean,max change (kT/e) : 1.9920906E-03 5.1322937E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 14:23:13 12.515u 0.489s 0:13.41 96.8% 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 Sat Oct 15 2011 at 14:23:13 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.893002 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 2.893002 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 530.7694 centred at (gu) : 87.28764 93.89769 86.61671 assigned negative charge : -527.7706 centred at (gu) : 87.39952 93.71101 86.93322 start vw surface at 0.1900000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 234539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26577 grid for indexing accessible points = 1.400000 m= 127059 mr = 178197 m= 49059 mr = 106398 m= 12705 mr = 40206 m= 1924 mr = 9689 m= 125 mr = 1236 m= 0 mr = 59 time to grow re-entrant surface = 1.750000 no. cavity mid-points inaccessible to solvent = 6194 time to turn everything in is 2.820000 number of dielectric boundary points 89626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 3.000000 number of grid points assigned charge 26424 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) : 1.928668 object centre at (A) : 37.49150 -15.45050 58.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3972822 0.1891478 midg,1,midg; midg,igrid,midg -5.9127815E-02 0.3503545 1,midg,midg; igrid,midg,midg 0.2270660 0.5454035 gauss-seidel spectral radius is 0.9992932 estimated iterations to convergence 297 setup time was (sec) 3.230000 now iterating at: 14:23:17 rms-change max change #iterations 12.02180 516.4204 at 10iterations 7.182483 146.5002 at 20iterations 4.271264 100.0863 at 30iterations 2.522766 47.73217 at 40iterations 1.491611 27.00774 at 50iterations 0.8776195 15.40013 at 60iterations 0.5159032 8.706989 at 70iterations 0.3022513 5.107881 at 80iterations 0.1773549 3.049332 at 90iterations 0.1041019 1.787943 at 100iterations 6.0909912E-02 1.008869 at 110iterations 3.5648193E-02 0.5711355 at 120iterations 2.0857394E-02 0.3168230 at 130iterations 1.2201115E-02 0.1849947 at 140iterations 7.1496726E-03 0.1094894 at 150iterations 4.1878638E-03 6.5700531E-02 at 160iterations 2.4682079E-03 4.1114330E-02 at 170iterations 1.4673515E-03 2.4070740E-02 at 180iterations finished qdiffx linear iterations at : 14:23:35 total time elapsed so far: 21.33000 # loops : 180 mean,max change (kT/e) : 1.4673515E-03 2.4070740E-02 energy calculations done at 21.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.54000 DelPhi exited at 14:23:36 21.543u 0.520s 0:22.40 98.4% 0+0k 0+0io 0pf+0w