Sun Oct 9 22:24:37 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+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 Sun Oct 9 2011 at 22:24:37 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6407257 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): 8.228000 62.83400 ymin,ymax (A): -38.76300 16.79900 zmin,zma (A): -3.892000 49.13000 x,y,z range (A): 54.60600 55.56200 53.02200 scale (grids/A): 0.6407257 object centre (A): 35.53100 -10.98200 22.61900 number of atom coordinates read : 2583 total number of charged atoms : 2436 net assigned charge : 4.525008 assigned positive charge : 391.1649 centred at (gu) : 90.26640 91.20207 90.22446 assigned negative charge : -386.6406 centred at (gu) : 90.30679 91.27682 90.25797 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6979 nv = 96 ne = 84 npr = 52403 no. pairs analyzed = 52403 no. exposed pairs = 3176 no. arc points = 22270 no. surface atoms = 1077 nbur = 1506 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 3774 m= 0 mr = 52 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2000000 number of dielectric boundary points 3541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8481 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0318082E-08 3.0115275E-09 midg,1,midg; midg,igrid,midg 1.2130798E-08 -2.8007943E-09 1,midg,midg; igrid,midg,midg 1.0990000E-08 2.1653672E-09 gauss-seidel spectral radius is 0.9873787 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 22:24:38 rms-change max change #iterations 0.1482944 24.69595 at 10iterations 1.4611865E-02 2.194293 at 20iterations 1.4633611E-03 0.2222633 at 30iterations 1.4496721E-04 2.0416260E-02 at 40iterations 1.4862487E-05 2.1629333E-03 at 50iterations finished qdiffx linear iterations at : 22:24:40 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.4862487E-05 2.1629333E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 22:24:41 3.390u 0.176s 0:03.85 92.4% 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 22:24:41 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.922177 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): 8.228000 62.83400 ymin,ymax (A): -38.76300 16.79900 zmin,zma (A): -3.892000 49.13000 x,y,z range (A): 54.60600 55.56200 53.02200 scale (grids/A): 1.922177 object centre (A): 35.53100 -10.98200 22.61900 number of atom coordinates read : 2583 total number of charged atoms : 2436 net assigned charge : 4.525008 assigned positive charge : 391.1649 centred at (gu) : 90.79842 93.60571 90.67277 assigned negative charge : -386.6406 centred at (gu) : 90.92030 93.83027 90.77359 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 75433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22270 grid for indexing accessible points = 1.400000 m= 25883 mr = 51774 m= 4194 mr = 18685 m= 296 mr = 2634 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1505 time to turn everything in is 0.3900000 number of dielectric boundary points 32582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19196 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) : 0.6407257 object centre at (A) : 35.53100 -10.98200 22.61900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8435620E-02 -6.4273803E-03 midg,1,midg; midg,igrid,midg -7.1001630E-03 2.0289065E-02 1,midg,midg; igrid,midg,midg -3.8333305E-03 4.9134060E-03 gauss-seidel spectral radius is 0.9986529 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 22:24:42 rms-change max change #iterations 4.266227 196.8756 at 10iterations 2.010227 67.66522 at 20iterations 0.9488844 32.96982 at 30iterations 0.4448912 13.72200 at 40iterations 0.2083134 6.395370 at 50iterations 9.8404288E-02 3.338236 at 60iterations 4.6228282E-02 1.391479 at 70iterations 2.1811591E-02 0.6880748 at 80iterations 1.0254235E-02 0.3300405 at 90iterations 4.8086308E-03 0.1641891 at 100iterations 2.2701547E-03 7.1676254E-02 at 110iterations 1.0657952E-03 3.4911156E-02 at 120iterations finished qdiffx linear iterations at : 22:24:50 total time elapsed so far: 8.570000 # loops : 120 mean,max change (kT/e) : 1.0657952E-03 3.4911156E-02 energy calculations done at 8.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.700000 DelPhi exited at 22:24:50 8.698u 0.191s 0:09.30 95.4% 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 22:24:50 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 2.883266 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): 8.228000 62.83400 ymin,ymax (A): -38.76300 16.79900 zmin,zma (A): -3.892000 49.13000 x,y,z range (A): 54.60600 55.56200 53.02200 scale (grids/A): 2.883266 object centre (A): 35.53100 -10.98200 22.61900 number of atom coordinates read : 2583 total number of charged atoms : 2436 net assigned charge : 4.525008 assigned positive charge : 391.1649 centred at (gu) : 91.19749 95.40845 91.00895 assigned negative charge : -386.6406 centred at (gu) : 91.38039 95.74531 91.16039 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 174685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22270 grid for indexing accessible points = 1.400000 m= 84891 mr = 125614 m= 29508 mr = 68820 m= 7614 mr = 23232 m= 1295 mr = 5818 m= 91 mr = 962 m= 3 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 4939 time to turn everything in is 0.9600000 number of dielectric boundary points 73593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19488 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) : 1.922177 object centre at (A) : 35.53100 -10.98200 22.61900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3820146 -0.2071991 midg,1,midg; midg,igrid,midg -0.2272486 0.2567424 1,midg,midg; igrid,midg,midg 3.8590308E-02 -0.1339968 gauss-seidel spectral radius is 0.9992670 estimated iterations to convergence 291 setup time was (sec) 1.190000 now iterating at: 22:24:52 rms-change max change #iterations 10.05618 373.0352 at 10iterations 5.863578 134.2672 at 20iterations 3.403417 66.36488 at 30iterations 1.969523 39.93144 at 40iterations 1.138359 22.14566 at 50iterations 0.6558325 13.79575 at 60iterations 0.3796141 7.632246 at 70iterations 0.2186208 4.271706 at 80iterations 0.1259684 2.509425 at 90iterations 7.2584070E-02 1.423485 at 100iterations 4.1684724E-02 0.7336102 at 110iterations 2.3996871E-02 0.4788904 at 120iterations 1.3830589E-02 0.2455235 at 130iterations 7.9660565E-03 0.1330032 at 140iterations 4.5784693E-03 8.0277681E-02 at 150iterations 2.6354378E-03 5.2417755E-02 at 160iterations 1.5159845E-03 2.7229309E-02 at 170iterations 8.7363709E-04 1.5760422E-02 at 180iterations finished qdiffx linear iterations at : 22:25:03 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 8.7363709E-04 1.5760422E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 22:25:04 12.731u 0.214s 0:13.25 97.6% 0+0k 0+0io 0pf+0w