Sun Oct 9 08:00:15 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 08:00:15 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 0.6954347 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): 4.622000 49.95600 ymin,ymax (A): -24.77000 26.42100 zmin,zma (A): -19.57300 30.28300 x,y,z range (A): 45.33400 51.19100 49.85600 scale (grids/A): 0.6954347 object centre (A): 27.28900 0.8254995 5.355000 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499990 assigned positive charge : 340.7554 centred at (gu) : 90.05396 91.02319 90.22495 assigned negative charge : -344.2557 centred at (gu) : 90.08427 91.10049 90.32861 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7459 nv = 96 ne = 84 npr = 44866 no. pairs analyzed = 44866 no. exposed pairs = 2882 no. arc points = 20814 no. surface atoms = 957 nbur = 1275 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 4100 m= 5 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2600000 number of dielectric boundary points 3801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1965 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8312 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0004901E-08 -6.8053069E-08 midg,1,midg; midg,igrid,midg 8.1297156E-09 -6.6127996E-08 1,midg,midg; igrid,midg,midg -8.9580547E-09 -3.4569506E-08 gauss-seidel spectral radius is 0.9892499 estimated iterations to convergence 79 setup time was (sec) 0.4700000 now iterating at: 08:00:16 rms-change max change #iterations 0.2011417 31.78736 at 10iterations 2.3595022E-02 3.880522 at 20iterations 2.8323892E-03 0.4190445 at 30iterations 3.3772740E-04 4.8156738E-02 at 40iterations 3.9857474E-05 5.5923462E-03 at 50iterations finished qdiffx linear iterations at : 08:00:18 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 3.9857474E-05 5.5923462E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 08:00:19 3.107u 0.138s 0:03.52 91.7% 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 08:00:19 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 2.086304 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): 4.622000 49.95600 ymin,ymax (A): -24.77000 26.42100 zmin,zma (A): -19.57300 30.28300 x,y,z range (A): 45.33400 51.19100 49.85600 scale (grids/A): 2.086304 object centre (A): 27.28900 0.8254995 5.355000 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499990 assigned positive charge : 340.7554 centred at (gu) : 90.16122 93.06931 90.67449 assigned negative charge : -344.2557 centred at (gu) : 90.25259 93.30148 90.98562 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20814 grid for indexing accessible points = 1.400000 m= 31597 mr = 53694 m= 6547 mr = 23811 m= 672 mr = 4487 m= 21 mr = 337 m= 0 mr = 1 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 917 time to turn everything in is 0.5700000 number of dielectric boundary points 34967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 16580 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) : 0.6954347 object centre at (A) : 27.28900 0.8254995 5.355000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3143168E-03 -4.1570041E-02 midg,1,midg; midg,igrid,midg 2.1642730E-02 -1.2111021E-03 1,midg,midg; igrid,midg,midg -1.4410676E-04 -3.4017485E-02 gauss-seidel spectral radius is 0.9988250 estimated iterations to convergence 231 setup time was (sec) 0.8400000 now iterating at: 08:00:20 rms-change max change #iterations 4.805599 193.9437 at 10iterations 2.367935 88.71783 at 20iterations 1.176806 39.00271 at 30iterations 0.5794879 18.76468 at 40iterations 0.2866057 9.058396 at 50iterations 0.1417584 4.451897 at 60iterations 6.9866136E-02 2.380209 at 70iterations 3.4579583E-02 0.9543209 at 80iterations 1.7143553E-02 0.5125628 at 90iterations 8.4569277E-03 0.2510338 at 100iterations 4.1860454E-03 0.1263466 at 110iterations 2.0689962E-03 6.2534809E-02 at 120iterations finished qdiffx linear iterations at : 08:00:26 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 2.0689962E-03 6.2534809E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 08:00:26 7.041u 0.152s 0:07.46 96.3% 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 08:00:26 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 3.129456 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): 4.622000 49.95600 ymin,ymax (A): -24.77000 26.42100 zmin,zma (A): -19.57300 30.28300 x,y,z range (A): 45.33400 51.19100 49.85600 scale (grids/A): 3.129456 object centre (A): 27.28900 0.8254995 5.355000 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499990 assigned positive charge : 340.7554 centred at (gu) : 90.24168 94.60393 91.01166 assigned negative charge : -344.2557 centred at (gu) : 90.37878 94.95213 91.47839 start vw surface at 0.1300000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 180520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20814 grid for indexing accessible points = 1.400000 m= 96547 mr = 129308 m= 40714 mr = 79561 m= 12616 mr = 33699 m= 2750 mr = 9877 m= 338 mr = 2037 m= 18 mr = 184 m= 0 mr = 3 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 3112 time to turn everything in is 1.770000 number of dielectric boundary points 78834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 16720 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) : 2.086304 object centre at (A) : 27.28900 0.8254995 5.355000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7524287E-02 -0.2741888 midg,1,midg; midg,igrid,midg 0.7821255 7.4136682E-02 1,midg,midg; igrid,midg,midg -2.7014229E-02 -0.2964947 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.050000 now iterating at: 08:00:29 rms-change max change #iterations 10.84002 387.8717 at 10iterations 6.386847 145.2921 at 20iterations 3.753598 76.44526 at 30iterations 2.201147 58.35144 at 40iterations 1.294124 24.49197 at 50iterations 0.7578083 17.62445 at 60iterations 0.4442560 8.657401 at 70iterations 0.2603517 4.579682 at 80iterations 0.1516207 2.534224 at 90iterations 8.8563621E-02 1.590438 at 100iterations 5.1769365E-02 1.002771 at 110iterations 3.0169196E-02 0.5180645 at 120iterations 1.7654950E-02 0.2823353 at 130iterations 1.0310707E-02 0.1845107 at 140iterations 6.0396818E-03 0.1077690 at 150iterations 3.5356760E-03 5.7138443E-02 at 160iterations 2.0805630E-03 3.6769867E-02 at 170iterations 1.2275989E-03 2.3258209E-02 at 180iterations finished qdiffx linear iterations at : 08:00:38 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 1.2275989E-03 2.3258209E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 08:00:39 12.050u 0.172s 0:12.49 97.8% 0+0k 0+0io 0pf+0w