Sat Oct 8 11:35:47 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+sph.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 = amb.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 Sat Oct 8 2011 at 11:35:47 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3355 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN6 602 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6534868 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): -23.28400 31.19300 ymin,ymax (A): -1.574000 51.94900 zmin,zma (A): 11.95100 59.64200 x,y,z range (A): 54.47700 53.52300 47.69100 scale (grids/A): 0.6534868 object centre (A): 3.954499 25.18750 35.79650 number of atom coordinates read : 3355 total number of charged atoms : 3224 net assigned charge : -3.499973 assigned positive charge : 512.7904 centred at (gu) : 90.76831 90.47937 89.08610 assigned negative charge : -516.2913 centred at (gu) : 90.81582 90.26961 89.24314 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9223 nv = 96 ne = 84 npr = 71418 no. pairs analyzed = 71418 no. exposed pairs = 3621 no. arc points = 24259 no. surface atoms = 1238 nbur = 2117 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 5697 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 411 time to turn everything in is 0.3500000 number of dielectric boundary points 3916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2331 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 11331 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2294345E-08 -3.5745039E-08 midg,1,midg; midg,igrid,midg -5.0166502E-08 4.1841918E-08 1,midg,midg; igrid,midg,midg 2.1788964E-09 -2.1724135E-08 gauss-seidel spectral radius is 0.9879143 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 11:35:48 rms-change max change #iterations 0.1968453 26.02810 at 10iterations 2.0634066E-02 2.778545 at 20iterations 2.1838967E-03 0.2686577 at 30iterations 2.3247158E-04 3.0094147E-02 at 40iterations 2.4236620E-05 2.8696060E-03 at 50iterations finished qdiffx linear iterations at : 11:35:51 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.4236620E-05 2.8696060E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 11:35:51 3.345u 0.173s 0:03.97 88.4% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 11:35:51 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3355 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN6 602 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.960460 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): -23.28400 31.19300 ymin,ymax (A): -1.574000 51.94900 zmin,zma (A): 11.95100 59.64200 x,y,z range (A): 54.47700 53.52300 47.69100 scale (grids/A): 1.960460 object centre (A): 3.954499 25.18750 35.79650 number of atom coordinates read : 3355 total number of charged atoms : 3224 net assigned charge : -3.499973 assigned positive charge : 512.7904 centred at (gu) : 92.30370 91.43702 87.25756 assigned negative charge : -516.2913 centred at (gu) : 92.44655 90.80843 87.72869 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 100345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24259 grid for indexing accessible points = 1.400000 m= 37971 mr = 74157 m= 6286 mr = 30199 m= 438 mr = 4403 m= 11 mr = 229 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 14399 time to turn everything in is 0.6800000 number of dielectric boundary points 36064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 25450 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) : 0.6534868 object centre at (A) : 3.954499 25.18750 35.79650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9289276E-03 -6.5414570E-02 midg,1,midg; midg,igrid,midg -5.4415468E-02 3.5979435E-02 1,midg,midg; igrid,midg,midg -1.3895682E-02 -2.3321131E-02 gauss-seidel spectral radius is 0.9987547 estimated iterations to convergence 224 setup time was (sec) 0.9800000 now iterating at: 11:35:53 rms-change max change #iterations 5.292261 198.8201 at 10iterations 2.563467 70.58976 at 20iterations 1.242610 36.06213 at 30iterations 0.6047724 16.79798 at 40iterations 0.2930857 8.267929 at 50iterations 0.1424558 4.144531 at 60iterations 6.9122992E-02 1.935123 at 70iterations 3.3613846E-02 0.8625412 at 80iterations 1.6321614E-02 0.4476261 at 90iterations 7.9126786E-03 0.2166615 at 100iterations 3.8444907E-03 0.1025124 at 110iterations 1.8733158E-03 5.2947998E-02 at 120iterations finished qdiffx linear iterations at : 11:35:59 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.8733158E-03 5.2947998E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 11:36:00 7.689u 0.209s 0:08.68 90.7% 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 Sat Oct 8 2011 at 11:36:00 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3355 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: ZN6 602 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.940691 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): -23.28400 31.19300 ymin,ymax (A): -1.574000 51.94900 zmin,zma (A): 11.95100 59.64200 x,y,z range (A): 54.47700 53.52300 47.69100 scale (grids/A): 2.940691 object centre (A): 3.954499 25.18750 35.79650 number of atom coordinates read : 3355 total number of charged atoms : 3224 net assigned charge : -3.499973 assigned positive charge : 512.7904 centred at (gu) : 93.45549 92.15542 85.88597 assigned negative charge : -516.2913 centred at (gu) : 93.66959 91.21259 86.59286 start vw surface at 0.1600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 232411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24259 grid for indexing accessible points = 1.400000 m= 122330 mr = 178643 m= 46315 mr = 104319 m= 11677 mr = 39606 m= 1940 mr = 9425 m= 136 mr = 1487 m= 5 mr = 68 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 46570 time to turn everything in is 1.740000 number of dielectric boundary points 81265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 25792 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) : 1.960460 object centre at (A) : 3.954499 25.18750 35.79650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6228421E-02 -0.7712976 midg,1,midg; midg,igrid,midg -0.4870369 0.3790344 1,midg,midg; igrid,midg,midg -0.3526475 -0.2015415 gauss-seidel spectral radius is 0.9992891 estimated iterations to convergence 296 setup time was (sec) 2.060000 now iterating at: 11:36:02 rms-change max change #iterations 11.98362 388.1416 at 10iterations 7.019893 132.9375 at 20iterations 4.111534 71.83029 at 30iterations 2.401009 38.70328 at 40iterations 1.400437 22.55538 at 50iterations 0.8147336 13.00604 at 60iterations 0.4752114 7.811143 at 70iterations 0.2760720 4.356575 at 80iterations 0.1607478 2.271393 at 90iterations 9.3528084E-02 1.729878 at 100iterations 5.4337732E-02 0.8300152 at 110iterations 3.1630978E-02 0.4638557 at 120iterations 1.8391177E-02 0.2962265 at 130iterations 1.0687596E-02 0.1830635 at 140iterations 6.2134895E-03 9.7326279E-02 at 150iterations 3.6114082E-03 5.3115368E-02 at 160iterations 2.0978618E-03 3.1505585E-02 at 170iterations 1.2213149E-03 1.8840790E-02 at 180iterations finished qdiffx linear iterations at : 11:36:13 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 1.2213149E-03 1.8840790E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 11:36:14 13.027u 0.232s 0:13.67 96.9% 0+0k 0+0io 0pf+0w