Sun Oct 9 06:02:15 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 06:02:15 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 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: 0.6867151 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): 15.54500 67.38600 ymin,ymax (A): 26.67400 77.60201 zmin,zma (A): 47.75000 89.03699 x,y,z range (A): 51.84100 50.92801 41.28699 scale (grids/A): 0.6867151 object centre (A): 41.46550 52.13800 68.39349 number of atom coordinates read : 1747 total number of charged atoms : 1603 net assigned charge : -5.293987 assigned positive charge : 267.1192 centred at (gu) : 90.70325 91.45077 90.61964 assigned negative charge : -272.4132 centred at (gu) : 90.80818 91.91032 90.67850 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5665 nv = 96 ne = 84 npr = 35683 no. pairs analyzed = 35683 no. exposed pairs = 2236 no. arc points = 15798 no. surface atoms = 755 nbur = 992 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3079 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2400000 number of dielectric boundary points 2875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1468 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6300 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7646076E-09 -4.5252268E-08 midg,1,midg; midg,igrid,midg 6.8845750E-08 -2.0587886E-07 1,midg,midg; igrid,midg,midg 2.8181135E-09 -6.0464181E-08 gauss-seidel spectral radius is 0.9889283 estimated iterations to convergence 77 setup time was (sec) 0.4400000 now iterating at: 06:02:15 rms-change max change #iterations 0.1674606 30.98428 at 10iterations 1.9479396E-02 3.183609 at 20iterations 2.1768054E-03 0.3395346 at 30iterations 2.5331770E-04 3.7163258E-02 at 40iterations 2.8419505E-05 3.7746429E-03 at 50iterations finished qdiffx linear iterations at : 06:02:18 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 2.8419505E-05 3.7746429E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 06:02:18 3.068u 0.146s 0:03.47 92.2% 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 06:02:18 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 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: 2.060145 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): 15.54500 67.38600 ymin,ymax (A): 26.67400 77.60201 zmin,zma (A): 47.75000 89.03699 x,y,z range (A): 51.84100 50.92801 41.28699 scale (grids/A): 2.060145 object centre (A): 41.46550 52.13800 68.39349 number of atom coordinates read : 1747 total number of charged atoms : 1603 net assigned charge : -5.293987 assigned positive charge : 267.1192 centred at (gu) : 92.10993 94.35229 91.85906 assigned negative charge : -272.4132 centred at (gu) : 92.42471 95.73096 92.03555 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15798 grid for indexing accessible points = 1.400000 m= 22797 mr = 40413 m= 4368 mr = 17309 m= 360 mr = 3029 m= 8 mr = 213 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 761 time to turn everything in is 0.4600000 number of dielectric boundary points 26281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 12723 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) : 0.6867151 object centre at (A) : 41.46550 52.13800 68.39349 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9662217E-03 -2.8298223E-02 midg,1,midg; midg,igrid,midg 6.8258159E-02 -7.2269298E-02 1,midg,midg; igrid,midg,midg -2.1432858E-02 -5.3758953E-02 gauss-seidel spectral radius is 0.9987378 estimated iterations to convergence 223 setup time was (sec) 0.7300000 now iterating at: 06:02:19 rms-change max change #iterations 4.140573 238.6616 at 10iterations 1.996825 73.37457 at 20iterations 0.9638243 30.87498 at 30iterations 0.4635599 15.88440 at 40iterations 0.2237700 7.374235 at 50iterations 0.1076206 3.593922 at 60iterations 5.2029178E-02 1.849373 at 70iterations 2.5132207E-02 0.7969818 at 80iterations 1.2107481E-02 0.4412975 at 90iterations 5.8332365E-03 0.1976982 at 100iterations 2.8165353E-03 9.7632587E-02 at 110iterations 1.3592021E-03 4.7082901E-02 at 120iterations finished qdiffx linear iterations at : 06:02:25 total time elapsed so far: 6.570000 # loops : 120 mean,max change (kT/e) : 1.3592021E-03 4.7082901E-02 energy calculations done at 6.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.730000 DelPhi exited at 06:02:26 6.733u 0.161s 0:07.25 95.0% 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 06:02:26 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 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: 3.090218 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): 15.54500 67.38600 ymin,ymax (A): 26.67400 77.60201 zmin,zma (A): 47.75000 89.03699 x,y,z range (A): 51.84100 50.92801 41.28699 scale (grids/A): 3.090218 object centre (A): 41.46550 52.13800 68.39349 number of atom coordinates read : 1747 total number of charged atoms : 1603 net assigned charge : -5.293987 assigned positive charge : 267.1192 centred at (gu) : 93.16495 96.52852 92.78872 assigned negative charge : -272.4132 centred at (gu) : 93.63713 98.59650 93.05344 start vw surface at 0.1400000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 137419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15798 grid for indexing accessible points = 1.400000 m= 71250 mr = 97583 m= 29029 mr = 58921 m= 8229 mr = 24092 m= 1547 mr = 6574 m= 188 mr = 1207 m= 9 mr = 140 m= 0 mr = 6 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 2432 time to turn everything in is 1.370000 number of dielectric boundary points 59148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 12824 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) : 2.060145 object centre at (A) : 41.46550 52.13800 68.39349 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1829293 -0.2119672 midg,1,midg; midg,igrid,midg 0.6188037 -0.5366085 1,midg,midg; igrid,midg,midg -0.2338544 -0.6032113 gauss-seidel spectral radius is 0.9992738 estimated iterations to convergence 293 setup time was (sec) 1.630000 now iterating at: 06:02:27 rms-change max change #iterations 9.342454 395.3257 at 10iterations 5.400992 124.7525 at 20iterations 3.128206 68.19389 at 30iterations 1.807306 39.18018 at 40iterations 1.044758 20.52292 at 50iterations 0.6033021 11.98325 at 60iterations 0.3491454 7.013184 at 70iterations 0.2009752 4.009483 at 80iterations 0.1159885 2.351126 at 90iterations 6.6995539E-02 1.396015 at 100iterations 3.8666371E-02 0.7810078 at 110iterations 2.2275796E-02 0.4827881 at 120iterations 1.2855272E-02 0.2634068 at 130iterations 7.4244640E-03 0.1343949 at 140iterations 4.2809406E-03 8.7722778E-02 at 150iterations 2.4730689E-03 5.1178932E-02 at 160iterations 1.4338103E-03 3.1140327E-02 at 170iterations 8.3064847E-04 2.0149231E-02 at 180iterations finished qdiffx linear iterations at : 06:02:37 total time elapsed so far: 10.78000 # loops : 180 mean,max change (kT/e) : 8.3064847E-04 2.0149231E-02 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 06:02:37 10.960u 0.171s 0:11.39 97.7% 0+0k 0+0io 0pf+0w