Mon Oct 10 14:38:16 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 Mon Oct 10 2011 at 14:38:16 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7441939 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): 47.36700 92.24700 ymin,ymax (A): -8.938000 36.74100 zmin,zma (A): -3.637000 44.20000 x,y,z range (A): 44.88000 45.67900 47.83700 scale (grids/A): 0.7441939 object centre (A): 69.80700 13.90150 20.28150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 89.15289 90.61790 90.16325 assigned negative charge : -320.2120 centred at (gu) : 89.16472 90.64952 90.31790 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7955 nv = 96 ne = 84 npr = 43719 no. pairs analyzed = 43719 no. exposed pairs = 2655 no. arc points = 18647 no. surface atoms = 898 nbur = 1207 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 4428 m= 4 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2900000 number of dielectric boundary points 3970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1558 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0306918E-08 -2.7773734E-07 midg,1,midg; midg,igrid,midg -5.4809107E-08 -1.4655100E-07 1,midg,midg; igrid,midg,midg -9.6205738E-08 -9.3535405E-08 gauss-seidel spectral radius is 0.9905885 estimated iterations to convergence 84 setup time was (sec) 0.5900000 now iterating at: 14:38:17 rms-change max change #iterations 0.2501684 31.59816 at 10iterations 3.3729464E-02 4.117606 at 20iterations 4.5260754E-03 0.6555939 at 30iterations 6.2340609E-04 7.8687668E-02 at 40iterations 8.6029781E-05 1.1817932E-02 at 50iterations finished qdiffx linear iterations at : 14:38:21 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 8.6029781E-05 1.1817932E-02 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 14:38:22 4.619u 0.354s 0:05.65 87.7% 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 14:38:22 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.232582 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): 47.36700 92.24700 ymin,ymax (A): -8.938000 36.74100 zmin,zma (A): -3.637000 44.20000 x,y,z range (A): 44.88000 45.67900 47.83700 scale (grids/A): 2.232582 object centre (A): 69.80700 13.90150 20.28150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 87.45848 91.85368 90.48960 assigned negative charge : -320.2120 centred at (gu) : 87.49437 91.94869 90.95379 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18647 grid for indexing accessible points = 1.400000 m= 33303 mr = 57660 m= 7049 mr = 25292 m= 717 mr = 4934 m= 17 mr = 420 m= 0 mr = 2 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 739 time to turn everything in is 0.6900000 number of dielectric boundary points 36403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15679 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) : 0.7441939 object centre at (A) : 69.80700 13.90150 20.28150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0705808E-03 -0.1330660 midg,1,midg; midg,igrid,midg -1.9451842E-02 -3.9137769E-02 1,midg,midg; igrid,midg,midg -1.0065066E-02 5.6148693E-03 gauss-seidel spectral radius is 0.9989337 estimated iterations to convergence 242 setup time was (sec) 1.040000 now iterating at: 14:38:23 rms-change max change #iterations 5.117727 211.2156 at 10iterations 2.596059 93.17301 at 20iterations 1.327913 39.82113 at 30iterations 0.6804467 19.34821 at 40iterations 0.3468473 12.02630 at 50iterations 0.1772453 5.113447 at 60iterations 9.0287909E-02 2.961786 at 70iterations 4.6305995E-02 1.312814 at 80iterations 2.3600781E-02 0.7656937 at 90iterations 1.2113373E-02 0.3442383 at 100iterations 6.1775320E-03 0.1663437 at 110iterations 3.1527053E-03 8.9163780E-02 at 120iterations finished qdiffx linear iterations at : 14:38:34 total time elapsed so far: 11.76000 # loops : 120 mean,max change (kT/e) : 3.1527053E-03 8.9163780E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 14:38:35 11.933u 0.461s 0:12.65 97.9% 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 14:38:35 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.348872 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): 47.36700 92.24700 ymin,ymax (A): -8.938000 36.74100 zmin,zma (A): -3.637000 44.20000 x,y,z range (A): 44.88000 45.67900 47.83700 scale (grids/A): 3.348872 object centre (A): 69.80700 13.90150 20.28150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 86.18781 92.78055 90.73441 assigned negative charge : -320.2120 centred at (gu) : 86.24152 92.92307 91.43075 start vw surface at 0.1100000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 192775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18647 grid for indexing accessible points = 1.400000 m= 102496 mr = 139266 m= 43599 mr = 84887 m= 13550 mr = 36231 m= 2908 mr = 10777 m= 403 mr = 2289 m= 17 mr = 272 m= 0 mr = 11 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 2539 time to turn everything in is 2.250000 number of dielectric boundary points 82015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 15736 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) : 2.232582 object centre at (A) : 69.80700 13.90150 20.28150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1478066 -1.535715 midg,1,midg; midg,igrid,midg -0.1566133 -0.2531046 1,midg,midg; igrid,midg,midg -2.9434795E-02 3.5850991E-02 gauss-seidel spectral radius is 0.9993219 estimated iterations to convergence 303 setup time was (sec) 2.600000 now iterating at: 14:38:38 rms-change max change #iterations 11.03294 285.8945 at 10iterations 6.501066 130.8788 at 20iterations 3.843814 63.15493 at 30iterations 2.261153 37.49680 at 40iterations 1.333681 20.88306 at 50iterations 0.7846880 13.89193 at 60iterations 0.4615786 7.233706 at 70iterations 0.2717296 4.454823 at 80iterations 0.1598240 2.661991 at 90iterations 9.3864925E-02 1.565659 at 100iterations 5.5202048E-02 0.8759341 at 110iterations 3.2348987E-02 0.5170212 at 120iterations 1.9100804E-02 0.2975159 at 130iterations 1.1200442E-02 0.1741152 at 140iterations 6.5898420E-03 0.1071014 at 150iterations 3.8771632E-03 6.1046600E-02 at 160iterations 2.2778618E-03 3.6263466E-02 at 170iterations 1.3401255E-03 2.1171570E-02 at 180iterations finished qdiffx linear iterations at : 14:38:55 total time elapsed so far: 20.19000 # loops : 180 mean,max change (kT/e) : 1.3401255E-03 2.1171570E-02 energy calculations done at 20.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.36000 DelPhi exited at 14:38:56 20.361u 0.452s 0:21.82 95.3% 0+0k 0+0io 0pf+0w