Sun Oct 9 16:18:15 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 16:18:15 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 = 3062 !!! WARNING: MG3 345 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6285977 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): -14.98200 37.40500 ymin,ymax (A): 54.07200 107.0030 zmin,zma (A): -3.673000 52.96100 x,y,z range (A): 52.38700 52.93100 56.63400 scale (grids/A): 0.6285977 object centre (A): 11.21150 80.53750 24.64400 number of atom coordinates read : 3062 total number of charged atoms : 2918 net assigned charge : -3.099983 assigned positive charge : 452.8991 centred at (gu) : 90.28072 88.82081 91.38109 assigned negative charge : -456.0005 centred at (gu) : 90.31113 88.69513 91.42681 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7986 nv = 96 ne = 84 npr = 63097 no. pairs analyzed = 63097 no. exposed pairs = 3750 no. arc points = 26255 no. surface atoms = 1278 nbur = 1784 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 478 mr = 4384 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2610 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9873 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1119201E-09 -1.0199314E-08 midg,1,midg; midg,igrid,midg -2.0312193E-08 7.1902635E-09 1,midg,midg; igrid,midg,midg 3.4846206E-11 -6.3791838E-09 gauss-seidel spectral radius is 0.9869318 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 16:18:16 rms-change max change #iterations 0.1486245 20.63106 at 10iterations 1.4109590E-02 2.037539 at 20iterations 1.3860619E-03 0.2125175 at 30iterations 1.8846789E-04 2.9871941E-02 at 40iterations 6.0487597E-05 1.1785030E-02 at 50iterations finished qdiffx linear iterations at : 16:18:19 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 6.0487597E-05 1.1785030E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 16:18:19 3.419u 0.147s 0:03.85 92.2% 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 16:18:19 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 = 3062 !!! WARNING: MG3 345 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.885793 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): -14.98200 37.40500 ymin,ymax (A): 54.07200 107.0030 zmin,zma (A): -3.673000 52.96100 x,y,z range (A): 52.38700 52.93100 56.63400 scale (grids/A): 1.885793 object centre (A): 11.21150 80.53750 24.64400 number of atom coordinates read : 3062 total number of charged atoms : 2918 net assigned charge : -3.099983 assigned positive charge : 452.8991 centred at (gu) : 90.84121 86.46152 94.14256 assigned negative charge : -456.0005 centred at (gu) : 90.93323 86.08504 94.28030 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26255 grid for indexing accessible points = 1.400000 m= 31186 mr = 60145 m= 5220 mr = 22485 m= 316 mr = 3213 m= 7 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 718 time to turn everything in is 0.6300000 number of dielectric boundary points 37357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 22928 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) : 0.6285977 object centre at (A) : 11.21150 80.53750 24.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0274920E-02 6.0238196E-03 midg,1,midg; midg,igrid,midg -2.9855702E-02 -9.0236356E-03 1,midg,midg; igrid,midg,midg -2.6683085E-02 -2.2962904E-02 gauss-seidel spectral radius is 0.9986495 estimated iterations to convergence 216 setup time was (sec) 0.9100000 now iterating at: 16:18:20 rms-change max change #iterations 4.556555 171.0334 at 10iterations 2.130718 71.39933 at 20iterations 1.001697 29.39836 at 30iterations 0.4690852 14.56974 at 40iterations 0.2207637 7.328168 at 50iterations 0.1038847 3.206568 at 60iterations 4.8801959E-02 1.534414 at 70iterations 2.2944922E-02 0.6677574 at 80iterations 1.0811655E-02 0.3627644 at 90iterations 5.0925966E-03 0.1544647 at 100iterations 2.4179292E-03 7.0904732E-02 at 110iterations 1.1601669E-03 3.3851624E-02 at 120iterations finished qdiffx linear iterations at : 16:18:27 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 1.1601669E-03 3.3851624E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 16:18:27 7.605u 0.192s 0:08.13 95.8% 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 Sun Oct 9 2011 at 16:18:27 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 = 3062 !!! WARNING: MG3 345 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.828690 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): -14.98200 37.40500 ymin,ymax (A): 54.07200 107.0030 zmin,zma (A): -3.673000 52.96100 x,y,z range (A): 52.38700 52.93100 56.63400 scale (grids/A): 2.828690 object centre (A): 11.21150 80.53750 24.64400 number of atom coordinates read : 3062 total number of charged atoms : 2918 net assigned charge : -3.099983 assigned positive charge : 452.8991 centred at (gu) : 91.26162 84.69203 96.21378 assigned negative charge : -456.0005 centred at (gu) : 91.39979 84.12753 96.42027 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 200656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26255 grid for indexing accessible points = 1.400000 m= 100109 mr = 146414 m= 36945 mr = 80994 m= 9489 mr = 29244 m= 1400 mr = 7020 m= 89 mr = 913 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2254 time to turn everything in is 1.630000 number of dielectric boundary points 84063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 23342 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) : 1.885793 object centre at (A) : 11.21150 80.53750 24.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3677479 0.1481710 midg,1,midg; midg,igrid,midg -0.3084994 -0.2422182 1,midg,midg; igrid,midg,midg -0.3927162 -0.2739934 gauss-seidel spectral radius is 0.9992747 estimated iterations to convergence 293 setup time was (sec) 1.930000 now iterating at: 16:18:29 rms-change max change #iterations 10.77810 337.5974 at 10iterations 6.356762 132.0909 at 20iterations 3.715587 71.97042 at 30iterations 2.168141 41.92334 at 40iterations 1.264773 22.43936 at 50iterations 0.7343162 13.04899 at 60iterations 0.4272012 8.178967 at 70iterations 0.2477461 4.560715 at 80iterations 0.1435774 2.712353 at 90iterations 8.3321922E-02 1.614113 at 100iterations 4.8201505E-02 0.9785995 at 110iterations 2.7963791E-02 0.4568141 at 120iterations 1.6176499E-02 0.2924365 at 130iterations 9.3565304E-03 0.1588879 at 140iterations 5.4230648E-03 9.3547821E-02 at 150iterations 3.1437350E-03 5.5871964E-02 at 160iterations 1.8248924E-03 3.1004906E-02 at 170iterations 1.0663922E-03 2.0980835E-02 at 180iterations finished qdiffx linear iterations at : 16:18:40 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 1.0663922E-03 2.0980835E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 16:18:40 12.613u 0.189s 0:13.09 97.7% 0+0k 0+0io 0pf+0w