Mon Oct 10 19:33:06 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 19:33:06 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: 211 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 836 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.9820419 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): -26.63700 9.614000 ymin,ymax (A): -27.13100 7.101000 zmin,zma (A): -17.40600 17.19200 x,y,z range (A): 36.25100 34.23200 34.59800 scale (grids/A): 0.9820419 object centre (A): -8.511500 -10.01500 -0.1070004 number of atom coordinates read : 836 total number of charged atoms : 750 net assigned charge : 2.3096800E-06 assigned positive charge : 118.1921 centred at (gu) : 90.35107 90.67483 89.70809 assigned negative charge : -118.1919 centred at (gu) : 90.04484 90.72279 89.88780 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6395 nv = 96 ne = 84 npr = 15276 no. pairs analyzed = 15276 no. exposed pairs = 1302 no. arc points = 9477 no. surface atoms = 438 nbur = 398 mkacc time = 3.0000001E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 736 mr = 3337 m= 14 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 29 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 4357 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8707059E-06 -2.7223748E-06 midg,1,midg; midg,igrid,midg 6.6202961E-07 -8.4146706E-07 1,midg,midg; igrid,midg,midg -4.6347163E-06 4.8970292E-06 gauss-seidel spectral radius is 0.9944503 estimated iterations to convergence 108 setup time was (sec) 0.4000000 now iterating at: 19:33:06 rms-change max change #iterations 0.4116338 75.43166 at 10iterations 8.8181444E-02 11.52345 at 20iterations 1.8906260E-02 2.841274 at 30iterations 4.0205182E-03 0.5060871 at 40iterations 8.6467195E-04 0.1145687 at 50iterations finished qdiffx linear iterations at : 19:33:09 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 8.6467195E-04 0.1145687 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:33:10 3.384u 0.208s 0:04.77 75.0% 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 19:33:10 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: 211 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 836 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: 2.946126 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): -26.63700 9.614000 ymin,ymax (A): -27.13100 7.101000 zmin,zma (A): -17.40600 17.19200 x,y,z range (A): 36.25100 34.23200 34.59800 scale (grids/A): 2.946126 object centre (A): -8.511500 -10.01500 -0.1070004 number of atom coordinates read : 836 total number of charged atoms : 750 net assigned charge : 2.3096800E-06 assigned positive charge : 118.1921 centred at (gu) : 91.05312 92.02460 89.12445 assigned negative charge : -118.1919 centred at (gu) : 90.13445 92.16817 89.66331 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 9477 grid for indexing accessible points = 1.400000 m= 29841 mr = 41632 m= 10180 mr = 22944 m= 2246 mr = 7666 m= 312 mr = 1531 m= 27 mr = 181 m= 0 mr = 8 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 32414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 6000 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) : 0.9820419 object centre at (A) : -8.511500 -10.01500 -0.1070004 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8275779E-02 -6.3316807E-02 midg,1,midg; midg,igrid,midg 2.3583800E-02 -5.7342522E-02 1,midg,midg; igrid,midg,midg -3.2214236E-02 0.1167025 gauss-seidel spectral radius is 0.9992039 estimated iterations to convergence 280 setup time was (sec) 0.9000000 now iterating at: 19:33:12 rms-change max change #iterations 4.768174 334.6639 at 10iterations 2.658113 128.9169 at 20iterations 1.480966 51.98036 at 30iterations 0.8280039 24.41318 at 40iterations 0.4630583 15.27743 at 50iterations 0.2590617 6.925293 at 60iterations 0.1445093 4.093102 at 70iterations 8.0731586E-02 2.329674 at 80iterations 4.5239694E-02 1.542944 at 90iterations 2.5387552E-02 0.7462573 at 100iterations 1.4135956E-02 0.4262085 at 110iterations 7.9086171E-03 0.2357504 at 120iterations finished qdiffx linear iterations at : 19:33:19 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 7.9086171E-03 0.2357504 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 19:33:21 8.730u 0.240s 0:10.18 88.1% 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 19:33:21 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: 211 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 836 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: 4.419188 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): -26.63700 9.614000 ymin,ymax (A): -27.13100 7.101000 zmin,zma (A): -17.40600 17.19200 x,y,z range (A): 36.25100 34.23200 34.59800 scale (grids/A): 4.419188 object centre (A): -8.511500 -10.01500 -0.1070004 number of atom coordinates read : 836 total number of charged atoms : 750 net assigned charge : 2.3096800E-06 assigned positive charge : 118.1921 centred at (gu) : 91.57970 93.03685 88.68673 assigned negative charge : -118.1919 centred at (gu) : 90.20164 93.25229 89.49497 start vw surface at 0.1100000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 145719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 9477 grid for indexing accessible points = 1.400000 m= 82774 mr = 99833 m= 45998 mr = 68366 m= 21159 mr = 39171 m= 7606 mr = 17461 m= 2267 mr = 6108 m= 511 mr = 1758 m= 87 mr = 377 m= 14 mr = 68 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 72988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 6000 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) : 2.946126 object centre at (A) : -8.511500 -10.01500 -0.1070004 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2237976 -0.3066176 midg,1,midg; midg,igrid,midg 0.1655896 -0.4719530 1,midg,midg; igrid,midg,midg -3.9203987E-02 0.6058787 gauss-seidel spectral radius is 0.9993814 estimated iterations to convergence 317 setup time was (sec) 2.220000 now iterating at: 19:33:23 rms-change max change #iterations 9.366379 251.4111 at 10iterations 5.714175 143.8474 at 20iterations 3.456555 93.88761 at 30iterations 2.086816 38.06877 at 40iterations 1.260409 20.42875 at 50iterations 0.7605482 13.31598 at 60iterations 0.4594744 8.085002 at 70iterations 0.2770798 5.322464 at 80iterations 0.1667644 2.729975 at 90iterations 0.1007961 1.706255 at 100iterations 6.0539979E-02 0.9471664 at 110iterations 3.6539305E-02 0.5935612 at 120iterations 2.2000495E-02 0.3597412 at 130iterations 1.3287626E-02 0.2337122 at 140iterations 7.9991594E-03 0.1392987 at 150iterations 4.8162048E-03 7.8454494E-02 at 160iterations 2.8981899E-03 4.8229694E-02 at 170iterations 1.7490023E-03 3.2466888E-02 at 180iterations finished qdiffx linear iterations at : 19:33:35 total time elapsed so far: 13.55000 # loops : 180 mean,max change (kT/e) : 1.7490023E-03 3.2466888E-02 energy calculations done at 13.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 19:33:35 13.740u 0.296s 0:14.43 97.2% 0+0k 0+0io 0pf+0w