Sun Oct 9 07:59:51 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+sph.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 = amb.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 07:59:52 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: 276 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 : -3.499991 assigned positive charge : 338.7554 centred at (gu) : 90.05968 91.03178 90.23639 assigned negative charge : -342.2557 centred at (gu) : 90.09325 91.11651 90.34536 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 = 9.9999994E-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 = 0.1100000 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 2.1814307E-08 -7.0233789E-08 midg,1,midg; midg,igrid,midg 1.0454317E-08 -6.9784818E-08 1,midg,midg; igrid,midg,midg -7.6476807E-09 -3.5847638E-08 gauss-seidel spectral radius is 0.9892499 estimated iterations to convergence 79 setup time was (sec) 0.4700000 now iterating at: 07:59:52 rms-change max change #iterations 0.1985117 31.71578 at 10iterations 2.3369003E-02 3.761810 at 20iterations 2.7959452E-03 0.4112244 at 30iterations 3.3331988E-04 4.8034668E-02 at 40iterations 3.9455987E-05 5.7296753E-03 at 50iterations finished qdiffx linear iterations at : 07:59:55 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 3.9455987E-05 5.7296753E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 07:59:55 3.081u 0.143s 0:03.50 92.0% 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 07:59:55 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: 276 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= 9.0000004E-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 : -3.499991 assigned positive charge : 338.7554 centred at (gu) : 90.17843 93.09511 90.70879 assigned negative charge : -342.2557 centred at (gu) : 90.27964 93.34953 91.03590 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 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 = 0.2700000 no. cavity mid-points inaccessible to solvent = 917 time to turn everything in is 0.5800000 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 6.7659114E-03 -4.2721942E-02 midg,1,midg; midg,igrid,midg 2.3107087E-02 -3.2767502E-03 1,midg,midg; igrid,midg,midg 7.7562849E-04 -3.4527846E-02 gauss-seidel spectral radius is 0.9988250 estimated iterations to convergence 231 setup time was (sec) 0.8400000 now iterating at: 07:59:56 rms-change max change #iterations 4.766136 193.9437 at 10iterations 2.347615 88.71775 at 20iterations 1.167197 39.01205 at 30iterations 0.5746224 19.13285 at 40iterations 0.2841838 9.174591 at 50iterations 0.1406234 4.318376 at 60iterations 6.9303527E-02 2.338058 at 70iterations 3.4294602E-02 0.9637146 at 80iterations 1.7003629E-02 0.5016191 at 90iterations 8.3823428E-03 0.2499008 at 100iterations 4.1513494E-03 0.1263351 at 110iterations 2.0517560E-03 6.0901165E-02 at 120iterations finished qdiffx linear iterations at : 08:00:02 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 2.0517560E-03 6.0901165E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 08:00:03 7.017u 0.163s 0:07.44 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 08:00:03 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: 276 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 : -3.499991 assigned positive charge : 338.7554 centred at (gu) : 90.26747 94.64260 91.06312 assigned negative charge : -342.2557 centred at (gu) : 90.41933 95.02422 91.55382 start vw surface at 0.1300000 fill in re-entrant regions at 0.7800000 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 2.0840531E-02 -0.2859316 midg,1,midg; midg,igrid,midg 0.7949538 5.1429242E-02 1,midg,midg; igrid,midg,midg -1.8101189E-02 -0.3012036 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.050000 now iterating at: 08:00:05 rms-change max change #iterations 10.76509 387.8718 at 10iterations 6.341015 145.2968 at 20iterations 3.726758 73.96680 at 30iterations 2.185655 58.38741 at 40iterations 1.285408 24.48247 at 50iterations 0.7526942 17.61149 at 60iterations 0.4413552 8.760420 at 70iterations 0.2585347 4.573765 at 80iterations 0.1506321 2.519176 at 90iterations 8.8004820E-02 1.597078 at 100iterations 5.1436983E-02 1.022444 at 110iterations 2.9972021E-02 0.5225182 at 120iterations 1.7539248E-02 0.2863388 at 130iterations 1.0242222E-02 0.1801653 at 140iterations 5.9967781E-03 0.1044345 at 150iterations 3.5088088E-03 5.7024002E-02 at 160iterations 2.0631412E-03 3.6285400E-02 at 170iterations 1.2158275E-03 2.3082733E-02 at 180iterations finished qdiffx linear iterations at : 08:00:15 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 1.2158275E-03 2.3082733E-02 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 08:00:15 12.068u 0.188s 0:12.53 97.6% 0+0k 0+0io 0pf+0w