Tue Nov 22 14:12:03 PST 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 Tue Nov 22 2011 at 14:12:07 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.6474022 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): -34.40000 5.499000 ymin,ymax (A): -4.919000 46.39400 zmin,zma (A): -31.24400 23.74500 x,y,z range (A): 39.89900 51.31300 54.98900 scale (grids/A): 0.6474022 object centre (A): -14.45050 20.73750 -3.749500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.3999 centred at (gu) : 90.59144 87.41853 90.08216 assigned negative charge : -290.4002 centred at (gu) : 90.68745 87.30667 90.14054 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5649 nv = 96 ne = 84 npr = 40495 no. pairs analyzed = 40495 no. exposed pairs = 2502 no. arc points = 17359 no. surface atoms = 842 nbur = 1128 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 283 mr = 3107 m= 0 mr = 30 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1796 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6679 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1702279E-08 -4.3930382E-10 midg,1,midg; midg,igrid,midg -1.1194770E-08 1.0175659E-08 1,midg,midg; igrid,midg,midg 1.3958133E-08 -5.1221334E-09 gauss-seidel spectral radius is 0.9875812 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 14:12:10 rms-change max change #iterations 0.1339622 22.24917 at 10iterations 1.3369584E-02 2.166028 at 20iterations 1.3842994E-03 0.2059250 at 30iterations 1.3818988E-04 2.7338028E-02 at 40iterations 1.4376132E-05 2.3803711E-03 at 50iterations finished qdiffx linear iterations at : 14:12:20 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 1.4376132E-05 2.3803711E-03 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 14:12:21 3.733u 0.231s 0:14.74 26.8% 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 Tue Nov 22 2011 at 14:12:24 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.942207 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): -34.40000 5.499000 ymin,ymax (A): -4.919000 46.39400 zmin,zma (A): -31.24400 23.74500 x,y,z range (A): 39.89900 51.31300 54.98900 scale (grids/A): 1.942207 object centre (A): -14.45050 20.73750 -3.749500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.3999 centred at (gu) : 91.77435 82.25559 90.24651 assigned negative charge : -290.4002 centred at (gu) : 92.06232 81.92034 90.42171 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17359 grid for indexing accessible points = 1.400000 m= 21601 mr = 41952 m= 3100 mr = 16352 m= 142 mr = 1928 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1233 time to turn everything in is 0.3200000 number of dielectric boundary points 25478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14493 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) : 0.6474022 object centre at (A) : -14.45050 20.73750 -3.749500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1232384E-02 4.9180467E-02 midg,1,midg; midg,igrid,midg -3.7983027E-03 3.2350454E-02 1,midg,midg; igrid,midg,midg 9.2326039E-03 -4.8557352E-03 gauss-seidel spectral radius is 0.9986086 estimated iterations to convergence 212 setup time was (sec) 0.5500000 now iterating at: 14:12:28 rms-change max change #iterations 3.763799 176.0736 at 10iterations 1.752705 66.00244 at 20iterations 0.8135992 29.76730 at 30iterations 0.3777467 14.58187 at 40iterations 0.1754056 6.499737 at 50iterations 8.1877507E-02 2.846981 at 60iterations 3.7975404E-02 1.343626 at 70iterations 1.7658386E-02 0.5768433 at 80iterations 8.2046231E-03 0.2829361 at 90iterations 3.8086176E-03 0.1340790 at 100iterations 1.7667157E-03 6.6276550E-02 at 110iterations 8.2117831E-04 3.4011841E-02 at 120iterations finished qdiffx linear iterations at : 14:12:53 total time elapsed so far: 8.780000 # loops : 120 mean,max change (kT/e) : 8.2117831E-04 3.4011841E-02 energy calculations done at 8.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.910000 DelPhi exited at 14:12:54 8.910u 0.294s 0:31.09 29.5% 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 Tue Nov 22 2011 at 14:12:56 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.913310 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): -34.40000 5.499000 ymin,ymax (A): -4.919000 46.39400 zmin,zma (A): -31.24400 23.74500 x,y,z range (A): 39.89900 51.31300 54.98900 scale (grids/A): 2.913310 object centre (A): -14.45050 20.73750 -3.749500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.3999 centred at (gu) : 92.66151 78.38323 90.36974 assigned negative charge : -290.4002 centred at (gu) : 93.09347 77.88058 90.63251 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 140932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17359 grid for indexing accessible points = 1.400000 m= 70778 mr = 101803 m= 24828 mr = 58534 m= 5346 mr = 20304 m= 637 mr = 4045 m= 30 mr = 404 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 4220 time to turn everything in is 0.8200000 number of dielectric boundary points 57457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14704 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) : 1.942207 object centre at (A) : -14.45050 20.73750 -3.749500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5990553E-03 1.015261 midg,1,midg; midg,igrid,midg -8.9361675E-02 0.3540991 1,midg,midg; igrid,midg,midg 5.9603304E-02 -2.8810205E-02 gauss-seidel spectral radius is 0.9992388 estimated iterations to convergence 286 setup time was (sec) 1.080000 now iterating at: 14:13:02 rms-change max change #iterations 8.868431 341.9233 at 10iterations 5.101213 131.4693 at 20iterations 2.915411 63.24117 at 30iterations 1.663198 34.74868 at 40iterations 0.9506689 19.37781 at 50iterations 0.5406701 11.15403 at 60iterations 0.3082516 6.627087 at 70iterations 0.1754040 3.411263 at 80iterations 0.1000659 1.971045 at 90iterations 5.6897059E-02 1.251891 at 100iterations 3.2393783E-02 0.6414795 at 110iterations 1.8421192E-02 0.3716860 at 120iterations 1.0496074E-02 0.2165852 at 130iterations 5.9591313E-03 0.1257706 at 140iterations 3.3941097E-03 6.6661835E-02 at 150iterations 1.9306852E-03 4.7588348E-02 at 160iterations 1.0994799E-03 2.1104336E-02 at 170iterations 6.2391791E-04 1.2446404E-02 at 180iterations finished qdiffx linear iterations at : 14:13:39 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 6.2391791E-04 1.2446404E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.49000 DelPhi exited at 14:13:41 13.487u 0.274s 0:45.43 30.2% 0+0k 0+0io 0pf+0w