Sun Oct 9 10:14:54 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 Sun Oct 9 2011 at 10:14:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6655077 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): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 0.6655077 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.500015 assigned positive charge : 314.0916 centred at (gu) : 90.16734 92.64875 91.29704 assigned negative charge : -312.5923 centred at (gu) : 90.21777 92.47301 91.28671 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6724 nv = 96 ne = 84 npr = 43353 no. pairs analyzed = 43353 no. exposed pairs = 2940 no. arc points = 20849 no. surface atoms = 985 nbur = 1195 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3516 m= 6 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2500000 number of dielectric boundary points 3564 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1880 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7577 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2507432E-09 6.9260366E-09 midg,1,midg; midg,igrid,midg -1.6702874E-08 6.1132731E-08 1,midg,midg; igrid,midg,midg 1.2142614E-08 -5.9799521E-09 gauss-seidel spectral radius is 0.9882700 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 10:14:54 rms-change max change #iterations 0.1553984 22.79623 at 10iterations 1.6798818E-02 2.591761 at 20iterations 1.7871145E-03 0.2495613 at 30iterations 1.9436950E-04 3.1642914E-02 at 40iterations 2.1104572E-05 2.9621124E-03 at 50iterations finished qdiffx linear iterations at : 10:14:57 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 2.1104572E-05 2.9621124E-03 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 10:14:57 3.040u 0.137s 0:03.47 91.3% 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 Sun Oct 9 2011 at 10:14:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.996523 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): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 1.996523 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.500015 assigned positive charge : 314.0916 centred at (gu) : 90.50178 97.94637 93.89090 assigned negative charge : -312.5923 centred at (gu) : 90.65359 97.41942 93.86034 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20849 grid for indexing accessible points = 1.400000 m= 26079 mr = 47565 m= 4745 mr = 19082 m= 368 mr = 3118 m= 6 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 32621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 16166 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) : 0.6655077 object centre at (A) : 23.76850 -0.3795004 20.99350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7126987E-02 4.9482286E-02 midg,1,midg; midg,igrid,midg -4.7590169E-03 6.3802972E-02 1,midg,midg; igrid,midg,midg -1.8853210E-02 -3.2998897E-02 gauss-seidel spectral radius is 0.9987197 estimated iterations to convergence 221 setup time was (sec) 0.7600000 now iterating at: 10:14:58 rms-change max change #iterations 4.135211 232.3138 at 10iterations 1.983994 79.79370 at 20iterations 0.9551875 34.71360 at 30iterations 0.4585953 15.51705 at 40iterations 0.2205643 7.198387 at 50iterations 0.1061740 3.565229 at 60iterations 5.1016688E-02 1.768687 at 70iterations 2.4518432E-02 0.7722378 at 80iterations 1.1736622E-02 0.3569496 at 90iterations 5.6392453E-03 0.1880894 at 100iterations 2.7024196E-03 8.5681915E-02 at 110iterations 1.3000102E-03 4.1553020E-02 at 120iterations finished qdiffx linear iterations at : 10:15:04 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 1.3000102E-03 4.1553020E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 10:15:04 6.819u 0.167s 0:07.26 96.0% 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 Sun Oct 9 2011 at 10:15:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.994785 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): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 2.994785 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.500015 assigned positive charge : 314.0916 centred at (gu) : 90.75258 101.9194 95.83628 assigned negative charge : -312.5923 centred at (gu) : 90.98042 101.1292 95.79047 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 165061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20849 grid for indexing accessible points = 1.400000 m= 81608 mr = 115821 m= 31806 mr = 65897 m= 8842 mr = 25778 m= 1588 mr = 6729 m= 103 mr = 1146 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 73597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 16340 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) : 1.996523 object centre at (A) : 23.76850 -0.3795004 20.99350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7682642E-02 0.4993627 midg,1,midg; midg,igrid,midg -7.2236530E-02 0.4529064 1,midg,midg; igrid,midg,midg -0.2596675 -0.3088689 gauss-seidel spectral radius is 0.9992852 estimated iterations to convergence 295 setup time was (sec) 1.540000 now iterating at: 10:15:06 rms-change max change #iterations 9.504204 477.8452 at 10iterations 5.561480 163.3440 at 20iterations 3.249605 64.76581 at 30iterations 1.900472 45.22625 at 40iterations 1.105652 27.25513 at 50iterations 0.6422133 11.61094 at 60iterations 0.3731326 7.677374 at 70iterations 0.2164992 4.059598 at 80iterations 0.1257082 2.317388 at 90iterations 7.2898023E-02 1.293124 at 100iterations 4.2230349E-02 0.7444067 at 110iterations 2.4524603E-02 0.4563313 at 120iterations 1.4264924E-02 0.2475767 at 130iterations 8.2442453E-03 0.1498511 at 140iterations 4.7913766E-03 9.5092773E-02 at 150iterations 2.7763420E-03 4.9554825E-02 at 160iterations 1.6126803E-03 2.8681874E-02 at 170iterations 9.3217404E-04 1.7990589E-02 at 180iterations finished qdiffx linear iterations at : 10:15:16 total time elapsed so far: 10.90000 # loops : 180 mean,max change (kT/e) : 9.3217404E-04 1.7990589E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 10:15:16 11.078u 0.160s 0:11.50 97.6% 0+0k 0+0io 0pf+0w