Mon Oct 10 19:37:42 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 19:37:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3213 !!! WARNING: HIR 201 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: 0.5973154 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): -6.982000 51.38400 ymin,ymax (A): 37.46800 94.78400 zmin,zma (A): -20.40300 39.19700 x,y,z range (A): 58.36600 57.31601 59.60000 scale (grids/A): 0.5973154 object centre (A): 22.20100 66.12600 9.397001 number of atom coordinates read : 3213 total number of charged atoms : 3074 net assigned charge : 5.514014 assigned positive charge : 490.9479 centred at (gu) : 90.24656 90.77418 91.56537 assigned negative charge : -485.4348 centred at (gu) : 90.22430 90.90817 91.55592 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7627 nv = 96 ne = 84 npr = 64420 no. pairs analyzed = 64420 no. exposed pairs = 4233 no. arc points = 29554 no. surface atoms = 1426 nbur = 1787 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 3957 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3009 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2861719E-09 3.6879180E-09 midg,1,midg; midg,igrid,midg 6.4724346E-09 -4.2113073E-09 1,midg,midg; igrid,midg,midg 1.2016939E-09 3.3070671E-09 gauss-seidel spectral radius is 0.9855502 estimated iterations to convergence 68 setup time was (sec) 0.5500000 now iterating at: 19:37:43 rms-change max change #iterations 0.1208986 18.73610 at 10iterations 1.0053298E-02 1.542304 at 20iterations 8.4903976E-04 0.1203346 at 30iterations 7.2132818E-05 1.1459827E-02 at 40iterations 6.1340270E-06 1.0147095E-03 at 50iterations finished qdiffx linear iterations at : 19:37:45 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 6.1340270E-06 1.0147095E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 19:37:46 3.319u 0.231s 0:04.22 83.8% 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 Mon Oct 10 2011 at 19:37:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3213 !!! WARNING: HIR 201 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: 1.791946 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): -6.982000 51.38400 ymin,ymax (A): 37.46800 94.78400 zmin,zma (A): -20.40300 39.19700 x,y,z range (A): 58.36600 57.31601 59.60000 scale (grids/A): 1.791946 object centre (A): 22.20100 66.12600 9.397001 number of atom coordinates read : 3213 total number of charged atoms : 3074 net assigned charge : 5.514014 assigned positive charge : 490.9479 centred at (gu) : 90.73886 92.32162 94.69521 assigned negative charge : -485.4348 centred at (gu) : 90.67248 92.72402 94.66744 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29554 grid for indexing accessible points = 1.400000 m= 28689 mr = 55567 m= 3966 mr = 20249 m= 205 mr = 2209 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.5900000 number of dielectric boundary points 37239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 23961 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) : 0.5973154 object centre at (A) : 22.20100 66.12600 9.397001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0193073E-02 -7.2870445E-03 midg,1,midg; midg,igrid,midg 3.5143860E-02 1.2890595E-03 1,midg,midg; igrid,midg,midg 3.2397415E-02 -7.4132264E-04 gauss-seidel spectral radius is 0.9985248 estimated iterations to convergence 206 setup time was (sec) 0.8700000 now iterating at: 19:37:47 rms-change max change #iterations 4.264451 188.4459 at 10iterations 1.927201 66.51353 at 20iterations 0.8759356 27.82128 at 30iterations 0.3959888 11.68915 at 40iterations 0.1804241 6.296743 at 50iterations 8.1795715E-02 2.584308 at 60iterations 3.7154887E-02 1.174143 at 70iterations 1.6810890E-02 0.5526190 at 80iterations 7.6407935E-03 0.2391815 at 90iterations 3.4731396E-03 0.1039886 at 100iterations 1.5778102E-03 4.7805786E-02 at 110iterations 7.1903627E-04 2.2592545E-02 at 120iterations finished qdiffx linear iterations at : 19:37:54 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 7.1903627E-04 2.2592545E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 19:37:55 7.517u 0.252s 0:08.46 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 Mon Oct 10 2011 at 19:37:55 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3213 !!! WARNING: HIR 201 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: 2.687919 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): -6.982000 51.38400 ymin,ymax (A): 37.46800 94.78400 zmin,zma (A): -20.40300 39.19700 x,y,z range (A): 58.36600 57.31601 59.60000 scale (grids/A): 2.687919 object centre (A): 22.20100 66.12600 9.397001 number of atom coordinates read : 3213 total number of charged atoms : 3074 net assigned charge : 5.514014 assigned positive charge : 490.9479 centred at (gu) : 91.10812 93.48232 97.04281 assigned negative charge : -485.4348 centred at (gu) : 91.00872 94.08601 97.00120 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 190678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29554 grid for indexing accessible points = 1.400000 m= 94068 mr = 135451 m= 31985 mr = 74982 m= 6814 mr = 24814 m= 852 mr = 4664 m= 38 mr = 501 m= 0 mr = 1 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 1.470000 number of dielectric boundary points 84022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 24584 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) : 1.791946 object centre at (A) : 22.20100 66.12600 9.397001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1526948 -0.1049392 midg,1,midg; midg,igrid,midg 0.4464779 4.0071592E-02 1,midg,midg; igrid,midg,midg 0.4874494 -0.1143699 gauss-seidel spectral radius is 0.9992482 estimated iterations to convergence 288 setup time was (sec) 1.780000 now iterating at: 19:37:57 rms-change max change #iterations 10.43818 263.3977 at 10iterations 6.115916 144.5369 at 20iterations 3.550337 72.53539 at 30iterations 2.052817 39.47553 at 40iterations 1.183561 22.44576 at 50iterations 0.6802394 13.38958 at 60iterations 0.3898942 7.371258 at 70iterations 0.2237209 4.375446 at 80iterations 0.1284467 2.370377 at 90iterations 7.3639363E-02 1.300112 at 100iterations 4.2075530E-02 0.7865162 at 110iterations 2.4035649E-02 0.4674494 at 120iterations 1.3762068E-02 0.2453098 at 130iterations 7.8677544E-03 0.1483688 at 140iterations 4.4979500E-03 9.5758438E-02 at 150iterations 2.5670393E-03 4.7567308E-02 at 160iterations 1.4715532E-03 2.5344849E-02 at 170iterations 8.3978684E-04 1.6469002E-02 at 180iterations finished qdiffx linear iterations at : 19:38:07 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 8.3978684E-04 1.6469002E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 19:38:08 12.518u 0.251s 0:13.07 97.6% 0+0k 0+0io 0pf+0w