Mon Oct 10 19:32:49 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 Mon Oct 10 2011 at 19:32:49 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: HIT 1162 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5933036 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): -0.8560000 48.91300 ymin,ymax (A): -17.43100 42.57200 zmin,zma (A): -12.08800 32.48700 x,y,z range (A): 49.76900 60.00300 44.57500 scale (grids/A): 0.5933036 object centre (A): 24.02850 12.57050 10.19950 number of atom coordinates read : 2629 total number of charged atoms : 2493 net assigned charge : 8.014023 assigned positive charge : 389.7135 centred at (gu) : 89.28030 91.25057 90.02576 assigned negative charge : -381.7003 centred at (gu) : 89.30088 91.19933 89.98123 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6185 nv = 96 ne = 84 npr = 52657 no. pairs analyzed = 52657 no. exposed pairs = 3560 no. arc points = 24936 no. surface atoms = 1195 nbur = 1434 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 309 mr = 3102 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2483 ## 292 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4152272E-09 4.0331471E-09 midg,1,midg; midg,igrid,midg 9.4725394E-10 5.5870548E-09 1,midg,midg; igrid,midg,midg 3.9026560E-09 1.8160069E-09 gauss-seidel spectral radius is 0.9853086 estimated iterations to convergence 68 setup time was (sec) 0.5500000 now iterating at: 19:32:50 rms-change max change #iterations 0.1017638 18.29629 at 10iterations 8.2831811E-03 1.330759 at 20iterations 7.0499914E-04 0.1175671 at 30iterations 7.3922456E-05 1.3088226E-02 at 40iterations 1.2470417E-05 2.9754639E-03 at 50iterations finished qdiffx linear iterations at : 19:32:53 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.2470417E-05 2.9754639E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 19:32:53 3.453u 0.213s 0:04.13 88.6% 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 Mon Oct 10 2011 at 19:32:53 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: HIT 1162 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.779911 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): -0.8560000 48.91300 ymin,ymax (A): -17.43100 42.57200 zmin,zma (A): -12.08800 32.48700 x,y,z range (A): 49.76900 60.00300 44.57500 scale (grids/A): 1.779911 object centre (A): 24.02850 12.57050 10.19950 number of atom coordinates read : 2629 total number of charged atoms : 2493 net assigned charge : 8.014023 assigned positive charge : 389.7135 centred at (gu) : 87.84016 93.75091 90.07651 assigned negative charge : -381.7003 centred at (gu) : 87.90240 93.59766 89.94316 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24936 grid for indexing accessible points = 1.400000 m= 22171 mr = 44025 m= 2819 mr = 15123 m= 118 mr = 1450 m= 0 mr = 27 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 194 time to turn everything in is 0.4700000 number of dielectric boundary points 31183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19436 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) : 0.5933036 object centre at (A) : 24.02850 12.57050 10.19950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3764628E-03 1.4192503E-02 midg,1,midg; midg,igrid,midg -8.4508458E-05 -8.1674680E-03 1,midg,midg; igrid,midg,midg 2.8763190E-02 1.0979706E-02 gauss-seidel spectral radius is 0.9984502 estimated iterations to convergence 202 setup time was (sec) 0.7800000 now iterating at: 19:32:54 rms-change max change #iterations 3.691198 172.6525 at 10iterations 1.635701 60.75568 at 20iterations 0.7284203 24.11445 at 30iterations 0.3256834 10.64508 at 40iterations 0.1442803 4.983399 at 50iterations 6.4516582E-02 2.688543 at 60iterations 2.8662415E-02 0.9946060 at 70iterations 1.2741604E-02 0.4494925 at 80iterations 5.6837322E-03 0.2107620 at 90iterations 2.5286572E-03 0.1145055 at 100iterations 1.1327480E-03 4.0124893E-02 at 110iterations 5.0818030E-04 2.0351410E-02 at 120iterations finished qdiffx linear iterations at : 19:33:01 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 5.0818030E-04 2.0351410E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 19:33:02 7.775u 0.233s 0:08.34 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 Mon Oct 10 2011 at 19:33:02 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: HIT 1162 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.669866 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): -0.8560000 48.91300 ymin,ymax (A): -17.43100 42.57200 zmin,zma (A): -12.08800 32.48700 x,y,z range (A): 49.76900 60.00300 44.57500 scale (grids/A): 2.669866 object centre (A): 24.02850 12.57050 10.19950 number of atom coordinates read : 2629 total number of charged atoms : 2493 net assigned charge : 8.014023 assigned positive charge : 389.7135 centred at (gu) : 86.76005 95.62614 90.11459 assigned negative charge : -381.7003 centred at (gu) : 86.85349 95.39639 89.91471 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 154473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24936 grid for indexing accessible points = 1.400000 m= 73304 mr = 107794 m= 23680 mr = 57344 m= 4688 mr = 17899 m= 527 mr = 3106 m= 13 mr = 282 m= 0 mr = 2 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 626 time to turn everything in is 1.200000 number of dielectric boundary points 70258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 19936 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) : 1.779911 object centre at (A) : 24.02850 12.57050 10.19950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8867749E-02 0.1627912 midg,1,midg; midg,igrid,midg 8.2103245E-02 -5.6743938E-02 1,midg,midg; igrid,midg,midg 0.4014021 9.1717407E-02 gauss-seidel spectral radius is 0.9992167 estimated iterations to convergence 282 setup time was (sec) 1.490000 now iterating at: 19:33:04 rms-change max change #iterations 9.120512 320.5400 at 10iterations 5.294969 129.5810 at 20iterations 3.051240 69.40070 at 30iterations 1.743907 39.60187 at 40iterations 0.9966943 22.10481 at 50iterations 0.5680870 13.20039 at 60iterations 0.3224883 7.169838 at 70iterations 0.1831911 3.452711 at 80iterations 0.1039390 2.256165 at 90iterations 5.8857791E-02 1.297459 at 100iterations 3.3344433E-02 0.6742938 at 110iterations 1.8899364E-02 0.3942108 at 120iterations 1.0687961E-02 0.2098131 at 130iterations 6.0355375E-03 0.1350589 at 140iterations 3.4127915E-03 7.0566177E-02 at 150iterations 1.9317456E-03 3.7569046E-02 at 160iterations 1.0939620E-03 2.3643494E-02 at 170iterations 6.1840581E-04 1.2763977E-02 at 180iterations finished qdiffx linear iterations at : 19:33:14 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 6.1840581E-04 1.2763977E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 19:33:15 12.494u 0.247s 0:13.12 97.0% 0+0k 0+0io 0pf+0w