Mon Oct 10 23:52:38 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 23:52:38 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 = 2712 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5915194 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): 14.82800 75.01200 ymin,ymax (A): -10.88300 43.71200 zmin,zma (A): -7.584000 34.88200 x,y,z range (A): 60.18400 54.59500 42.46600 scale (grids/A): 0.5915194 object centre (A): 44.92000 16.41450 13.64900 number of atom coordinates read : 2712 total number of charged atoms : 2565 net assigned charge : 4.406022 assigned positive charge : 411.8957 centred at (gu) : 89.27077 89.80361 89.91795 assigned negative charge : -407.4903 centred at (gu) : 89.54813 89.93607 90.09189 start vw surface at 0.2400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 6117 nv = 96 ne = 84 npr = 55509 no. pairs analyzed = 55509 no. exposed pairs = 3179 no. arc points = 22247 no. surface atoms = 1077 nbur = 1635 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 268 mr = 3379 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.4800000 number of dielectric boundary points 2986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2203 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 7762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4945658E-09 -3.7721266E-09 midg,1,midg; midg,igrid,midg 5.4383498E-09 -2.4646958E-09 1,midg,midg; igrid,midg,midg 1.0968858E-08 -5.9343259E-09 gauss-seidel spectral radius is 0.9852160 estimated iterations to convergence 67 setup time was (sec) 0.7500000 now iterating at: 23:52:39 rms-change max change #iterations 0.1100026 16.61627 at 10iterations 9.4115091E-03 1.504746 at 20iterations 1.1344135E-03 0.2309494 at 30iterations 2.4895955E-04 6.1565399E-02 at 40iterations 6.5257969E-05 1.6796112E-02 at 50iterations finished qdiffx linear iterations at : 23:52:43 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 6.5257969E-05 1.6796112E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 23:52:43 4.170u 0.190s 0:04.84 90.0% 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 Mon Oct 10 2011 at 23:52:43 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 = 2712 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.774558 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): 14.82800 75.01200 ymin,ymax (A): -10.88300 43.71200 zmin,zma (A): -7.584000 34.88200 x,y,z range (A): 60.18400 54.59500 42.46600 scale (grids/A): 1.774558 object centre (A): 44.92000 16.41450 13.64900 number of atom coordinates read : 2712 total number of charged atoms : 2565 net assigned charge : 4.406022 assigned positive charge : 411.8957 centred at (gu) : 87.81169 89.41018 89.75359 assigned negative charge : -407.4903 centred at (gu) : 88.64400 89.80784 90.27527 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 67724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22247 grid for indexing accessible points = 1.400000 m= 22049 mr = 47404 m= 2745 mr = 16091 m= 105 mr = 1608 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 690 time to turn everything in is 0.6500000 number of dielectric boundary points 27502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19995 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) : 0.5915194 object centre at (A) : 44.92000 16.41450 13.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4571944E-02 4.4270675E-03 midg,1,midg; midg,igrid,midg 3.0657338E-02 -1.7674049E-02 1,midg,midg; igrid,midg,midg 6.4899382E-04 -5.8332309E-02 gauss-seidel spectral radius is 0.9984382 estimated iterations to convergence 201 setup time was (sec) 1.000000 now iterating at: 23:52:45 rms-change max change #iterations 3.839018 176.9447 at 10iterations 1.694744 62.65195 at 20iterations 0.7543233 28.25247 at 30iterations 0.3354387 11.13774 at 40iterations 0.1492799 5.196815 at 50iterations 6.6331886E-02 2.271622 at 60iterations 2.9510647E-02 0.9916992 at 70iterations 1.3230829E-02 0.4910202 at 80iterations 6.0033612E-03 0.2100601 at 90iterations 2.7789332E-03 9.8510742E-02 at 100iterations 1.3249435E-03 5.2635193E-02 at 110iterations 6.6470070E-04 2.9010773E-02 at 120iterations finished qdiffx linear iterations at : 23:52:53 total time elapsed so far: 9.000000 # loops : 120 mean,max change (kT/e) : 6.6470070E-04 2.9010773E-02 energy calculations done at 9.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.260000 DelPhi exited at 23:52:53 9.264u 0.199s 0:09.86 95.8% 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 23:52:53 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 = 2712 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.661837 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): 14.82800 75.01200 ymin,ymax (A): -10.88300 43.71200 zmin,zma (A): -7.584000 34.88200 x,y,z range (A): 60.18400 54.59500 42.46600 scale (grids/A): 2.661837 object centre (A): 44.92000 16.41450 13.64900 number of atom coordinates read : 2712 total number of charged atoms : 2565 net assigned charge : 4.406022 assigned positive charge : 411.8957 centred at (gu) : 86.71748 89.11507 89.63016 assigned negative charge : -407.4903 centred at (gu) : 87.96587 89.71169 90.41290 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 157081 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22247 grid for indexing accessible points = 1.400000 m= 74713 mr = 115215 m= 23261 mr = 60824 m= 4483 mr = 18443 m= 459 mr = 3245 m= 5 mr = 302 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 2266 time to turn everything in is 1.500000 number of dielectric boundary points 61973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 20514 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) : 1.774558 object centre at (A) : 44.92000 16.41450 13.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2773438 7.3261052E-02 midg,1,midg; midg,igrid,midg 0.4602508 -0.2989842 1,midg,midg; igrid,midg,midg -7.2119519E-02 -0.8333586 gauss-seidel spectral radius is 0.9992008 estimated iterations to convergence 279 setup time was (sec) 1.880000 now iterating at: 23:52:55 rms-change max change #iterations 9.216138 256.6675 at 10iterations 5.225563 114.6303 at 20iterations 2.949514 69.17443 at 30iterations 1.667549 35.20570 at 40iterations 0.9405128 18.62514 at 50iterations 0.5288213 11.97509 at 60iterations 0.2979020 6.069096 at 70iterations 0.1669901 3.229317 at 80iterations 9.4416454E-02 1.755812 at 90iterations 5.3042334E-02 1.011032 at 100iterations 2.9793521E-02 0.6161289 at 110iterations 1.6786391E-02 0.3145409 at 120iterations 9.5133055E-03 0.2139797 at 130iterations 5.3809541E-03 0.1080055 at 140iterations 3.0788798E-03 6.2984467E-02 at 150iterations 1.7831527E-03 4.2484283E-02 at 160iterations 1.0669946E-03 2.5226593E-02 at 170iterations 6.6118792E-04 1.6426086E-02 at 180iterations finished qdiffx linear iterations at : 23:53:10 total time elapsed so far: 16.47000 # loops : 180 mean,max change (kT/e) : 6.6118792E-04 1.6426086E-02 energy calculations done at 16.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.75000 DelPhi exited at 23:53:11 16.754u 0.225s 0:17.33 97.9% 0+0k 0+0io 0pf+0w