Sun Oct 9 06:54:11 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 06:54:11 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6891212 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): -0.2689999 44.79000 ymin,ymax (A): -13.91900 34.49200 zmin,zma (A): -28.10600 23.55400 x,y,z range (A): 45.05900 48.41100 51.66000 scale (grids/A): 0.6891212 object centre (A): 22.26050 10.28650 -2.275999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499988 assigned positive charge : 300.3900 centred at (gu) : 88.40176 90.56754 90.88226 assigned negative charge : -301.8900 centred at (gu) : 88.66113 90.60583 90.92221 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 42114 no. pairs analyzed = 42114 no. exposed pairs = 2481 no. arc points = 17558 no. surface atoms = 830 nbur = 1165 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3602 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 128 time to turn everything in is 0.2800000 number of dielectric boundary points 3137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1664 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7260 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6495772E-09 -2.6037759E-08 midg,1,midg; midg,igrid,midg 2.3940974E-09 -2.3849605E-08 1,midg,midg; igrid,midg,midg 9.7538582E-08 -6.7204411E-08 gauss-seidel spectral radius is 0.9890237 estimated iterations to convergence 78 setup time was (sec) 0.6000000 now iterating at: 06:54:12 rms-change max change #iterations 0.1852637 27.79944 at 10iterations 2.1566398E-02 3.013599 at 20iterations 2.4944996E-03 0.3899651 at 30iterations 2.9528132E-04 4.4735909E-02 at 40iterations 3.4028508E-05 4.9438477E-03 at 50iterations finished qdiffx linear iterations at : 06:54:15 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 3.4028508E-05 4.9438477E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 06:54:16 4.298u 0.300s 0:04.87 94.2% 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 06:54:16 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.067364 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): -0.2689999 44.79000 ymin,ymax (A): -13.91900 34.49200 zmin,zma (A): -28.10600 23.55400 x,y,z range (A): 45.05900 48.41100 51.66000 scale (grids/A): 2.067364 object centre (A): 22.26050 10.28650 -2.275999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499988 assigned positive charge : 300.3900 centred at (gu) : 85.20509 91.70243 92.64688 assigned negative charge : -301.8900 centred at (gu) : 85.98336 91.81753 92.76662 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 25092 mr = 47529 m= 4367 mr = 18780 m= 318 mr = 2898 m= 5 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2862 time to turn everything in is 0.6200000 number of dielectric boundary points 28839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14728 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) : 0.6891212 object centre at (A) : 22.26050 10.28650 -2.275999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9460577E-02 -4.9672440E-02 midg,1,midg; midg,igrid,midg -3.7985731E-02 -2.7832950E-02 1,midg,midg; igrid,midg,midg 7.9785272E-02 -3.5007168E-02 gauss-seidel spectral radius is 0.9987690 estimated iterations to convergence 226 setup time was (sec) 0.9700000 now iterating at: 06:54:17 rms-change max change #iterations 4.392955 199.7278 at 10iterations 2.124058 87.96693 at 20iterations 1.035021 31.72448 at 30iterations 0.5036774 16.82806 at 40iterations 0.2455474 7.660837 at 50iterations 0.1197308 3.800203 at 60iterations 5.8027811E-02 1.907953 at 70iterations 2.8217651E-02 0.9875317 at 80iterations 1.3796743E-02 0.4328136 at 90iterations 6.6684312E-03 0.2110772 at 100iterations 3.2423169E-03 0.1026988 at 110iterations 1.5816154E-03 5.0839424E-02 at 120iterations finished qdiffx linear iterations at : 06:54:26 total time elapsed so far: 9.880000 # loops : 120 mean,max change (kT/e) : 1.5816154E-03 5.0839424E-02 energy calculations done at 9.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.07000 DelPhi exited at 06:54:27 10.070u 0.349s 0:10.73 97.0% 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 06:54:27 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.101045 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): -0.2689999 44.79000 ymin,ymax (A): -13.91900 34.49200 zmin,zma (A): -28.10600 23.55400 x,y,z range (A): 45.05900 48.41100 51.66000 scale (grids/A): 3.101045 object centre (A): 22.26050 10.28650 -2.275999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499988 assigned positive charge : 300.3900 centred at (gu) : 82.80773 92.55386 93.97026 assigned negative charge : -301.8900 centred at (gu) : 83.97509 92.72633 94.14992 start vw surface at 0.1200000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 157936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 80715 mr = 114792 m= 30441 mr = 66704 m= 8206 mr = 24848 m= 1377 mr = 6370 m= 129 mr = 960 m= 1 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 9693 time to turn everything in is 1.700000 number of dielectric boundary points 65059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 14848 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) : 2.067364 object centre at (A) : 22.26050 10.28650 -2.275999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5384150 -0.5747485 midg,1,midg; midg,igrid,midg -0.5470372 -0.4151893 1,midg,midg; igrid,midg,midg 0.9534213 -0.2750316 gauss-seidel spectral radius is 0.9992833 estimated iterations to convergence 295 setup time was (sec) 2.050000 now iterating at: 06:54:29 rms-change max change #iterations 9.893010 422.9426 at 10iterations 5.736942 133.0597 at 20iterations 3.327058 63.44952 at 30iterations 1.927505 35.63100 at 40iterations 1.117359 21.17829 at 50iterations 0.6467879 12.02607 at 60iterations 0.3748459 7.393218 at 70iterations 0.2169852 4.568265 at 80iterations 0.1253422 2.346626 at 90iterations 7.2517201E-02 1.387448 at 100iterations 4.1971281E-02 0.7492981 at 110iterations 2.4335405E-02 0.4145699 at 120iterations 1.4092429E-02 0.2578068 at 130iterations 8.1181182E-03 0.1381893 at 140iterations 4.7130883E-03 8.5494429E-02 at 150iterations 2.7240517E-03 4.6863556E-02 at 160iterations 1.5751602E-03 2.8005004E-02 at 170iterations 9.1365905E-04 1.6180038E-02 at 180iterations finished qdiffx linear iterations at : 06:54:43 total time elapsed so far: 16.22000 # loops : 180 mean,max change (kT/e) : 9.1365905E-04 1.6180038E-02 energy calculations done at 16.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.41000 DelPhi exited at 06:54:44 16.410u 0.345s 0:17.03 98.3% 0+0k 0+0io 0pf+0w