Sat Oct 8 20:45:53 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 20:45:53 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 418 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6169309 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): -31.44700 17.43100 ymin,ymax (A): -23.25600 23.30500 zmin,zma (A): -12.51300 45.19200 x,y,z range (A): 48.87800 46.56100 57.70500 scale (grids/A): 0.6169309 object centre (A): -7.008000 2.4499893E-02 16.33950 number of atom coordinates read : 2555 total number of charged atoms : 2420 net assigned charge : 3.500008 assigned positive charge : 386.2631 centred at (gu) : 88.53465 89.07660 89.50565 assigned negative charge : -382.7636 centred at (gu) : 88.43946 89.10246 89.39560 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6360 nv = 96 ne = 84 npr = 52813 no. pairs analyzed = 52813 no. exposed pairs = 2966 no. arc points = 21228 no. surface atoms = 998 nbur = 1557 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3589 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.3800000 number of dielectric boundary points 3091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4658628E-09 8.2176790E-09 midg,1,midg; midg,igrid,midg 5.1652904E-09 9.3941244E-10 1,midg,midg; igrid,midg,midg -4.3482986E-09 6.0144836E-09 gauss-seidel spectral radius is 0.9863883 estimated iterations to convergence 70 setup time was (sec) 0.7000000 now iterating at: 20:45:54 rms-change max change #iterations 0.1203948 23.55267 at 10iterations 1.1157271E-02 1.670986 at 20iterations 1.0368897E-03 0.1629944 at 30iterations 1.0394418E-04 1.5650749E-02 at 40iterations 1.0898636E-05 1.6784668E-03 at 50iterations finished qdiffx linear iterations at : 20:45:58 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 1.0898636E-05 1.6784668E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 20:45:58 4.492u 0.454s 0:05.20 95.0% 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 Sat Oct 8 2011 at 20:45:59 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 418 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.850793 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): -31.44700 17.43100 ymin,ymax (A): -23.25600 23.30500 zmin,zma (A): -12.51300 45.19200 x,y,z range (A): 48.87800 46.56100 57.70500 scale (grids/A): 1.850793 object centre (A): -7.008000 2.4499893E-02 16.33950 number of atom coordinates read : 2555 total number of charged atoms : 2420 net assigned charge : 3.500008 assigned positive charge : 386.2631 centred at (gu) : 85.60387 87.22927 88.51645 assigned negative charge : -382.7636 centred at (gu) : 85.31818 87.30707 88.18654 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 69794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21228 grid for indexing accessible points = 1.400000 m= 24208 mr = 49044 m= 3353 mr = 17882 m= 151 mr = 2000 m= 0 mr = 48 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3388 time to turn everything in is 0.7500000 number of dielectric boundary points 28532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 18966 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) : 0.6169309 object centre at (A) : -7.008000 2.4499893E-02 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7862035E-02 2.2294963E-02 midg,1,midg; midg,igrid,midg 1.1999628E-02 1.7587922E-03 1,midg,midg; igrid,midg,midg -3.2207612E-03 2.9531006E-02 gauss-seidel spectral radius is 0.9985499 estimated iterations to convergence 208 setup time was (sec) 1.070000 now iterating at: 20:46:00 rms-change max change #iterations 3.954986 175.7331 at 10iterations 1.813833 60.18812 at 20iterations 0.8283290 29.92010 at 30iterations 0.3803396 13.33985 at 40iterations 0.1743606 6.289631 at 50iterations 8.0193542E-02 2.659346 at 60iterations 3.6621369E-02 1.174091 at 70iterations 1.6775478E-02 0.6021061 at 80iterations 7.6554534E-03 0.2488604 at 90iterations 3.5207865E-03 0.1232224 at 100iterations 1.6138285E-03 5.7252884E-02 at 110iterations 7.4142794E-04 2.6748657E-02 at 120iterations finished qdiffx linear iterations at : 20:46:09 total time elapsed so far: 10.05000 # loops : 120 mean,max change (kT/e) : 7.4142794E-04 2.6748657E-02 energy calculations done at 10.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 20:46:10 10.282u 0.458s 0:11.04 97.1% 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 Sat Oct 8 2011 at 20:46:10 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 418 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.776189 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): -31.44700 17.43100 ymin,ymax (A): -23.25600 23.30500 zmin,zma (A): -12.51300 45.19200 x,y,z range (A): 48.87800 46.56100 57.70500 scale (grids/A): 2.776189 object centre (A): -7.008000 2.4499893E-02 16.33950 number of atom coordinates read : 2555 total number of charged atoms : 2420 net assigned charge : 3.500008 assigned positive charge : 386.2631 centred at (gu) : 83.40552 85.84374 87.77470 assigned negative charge : -382.7636 centred at (gu) : 82.97723 85.96046 87.27963 start vw surface at 0.1400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 161503 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21228 grid for indexing accessible points = 1.400000 m= 80516 mr = 118611 m= 26827 mr = 66329 m= 5772 mr = 21321 m= 642 mr = 4236 m= 21 mr = 393 m= 0 mr = 7 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 11883 time to turn everything in is 1.790000 number of dielectric boundary points 64384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 19359 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) : 1.850793 object centre at (A) : -7.008000 2.4499893E-02 16.33950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1883124E-02 0.2813793 midg,1,midg; midg,igrid,midg 0.1438616 6.8721414E-04 1,midg,midg; igrid,midg,midg -3.7863076E-02 0.3963586 gauss-seidel spectral radius is 0.9992286 estimated iterations to convergence 284 setup time was (sec) 2.140000 now iterating at: 20:46:12 rms-change max change #iterations 9.321683 320.9865 at 10iterations 5.350898 110.3542 at 20iterations 3.051997 67.04113 at 30iterations 1.736232 34.31026 at 40iterations 0.9902316 19.64148 at 50iterations 0.5621284 10.66711 at 60iterations 0.3201759 5.921852 at 70iterations 0.1817659 3.345490 at 80iterations 0.1031382 1.997075 at 90iterations 5.8559965E-02 1.077835 at 100iterations 3.3251502E-02 0.5991211 at 110iterations 1.8936036E-02 0.3864479 at 120iterations 1.0727821E-02 0.1998158 at 130iterations 6.0919686E-03 0.1156540 at 140iterations 3.4626615E-03 6.9307327E-02 at 150iterations 1.9712946E-03 3.6969185E-02 at 160iterations 1.1207744E-03 2.2630692E-02 at 170iterations 6.4269063E-04 1.1924028E-02 at 180iterations finished qdiffx linear iterations at : 20:46:27 total time elapsed so far: 16.95000 # loops : 180 mean,max change (kT/e) : 6.4269063E-04 1.1924028E-02 energy calculations done at 16.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.16000 DelPhi exited at 20:46:28 17.168u 0.506s 0:18.03 97.9% 0+0k 0+0io 0pf+0w