Tue Oct 11 06:39:30 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 Tue Oct 11 2011 at 06:39:30 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.6726245 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): -20.56000 23.65500 ymin,ymax (A): -26.74300 10.72500 zmin,zma (A): -16.37400 36.55300 x,y,z range (A): 44.21500 37.46800 52.92700 scale (grids/A): 0.6726245 object centre (A): 1.547501 -8.009001 10.08950 number of atom coordinates read : 2056 total number of charged atoms : 1922 net assigned charge : 6.931010 assigned positive charge : 312.1291 centred at (gu) : 90.15096 90.84360 90.14827 assigned negative charge : -305.1981 centred at (gu) : 89.97826 90.82323 90.14046 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6188 nv = 96 ne = 84 npr = 41685 no. pairs analyzed = 41685 no. exposed pairs = 2441 no. arc points = 16896 no. surface atoms = 836 nbur = 1220 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3514 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1716 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2231946E-08 2.7007797E-08 midg,1,midg; midg,igrid,midg 1.7156035E-08 3.4206224E-08 1,midg,midg; igrid,midg,midg -1.2571285E-08 6.2707215E-08 gauss-seidel spectral radius is 0.9884859 estimated iterations to convergence 76 setup time was (sec) 0.3500000 now iterating at: 06:39:30 rms-change max change #iterations 0.1614915 23.48619 at 10iterations 1.8764362E-02 2.694064 at 20iterations 2.2353055E-03 0.3203430 at 30iterations 3.3517598E-04 4.4174194E-02 at 40iterations 7.2743744E-05 1.1655807E-02 at 50iterations finished qdiffx linear iterations at : 06:39:33 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 7.2743744E-05 1.1655807E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:39:33 3.341u 0.175s 0:03.92 89.5% 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 Oct 11 2011 at 06:39:34 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.017874 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): -20.56000 23.65500 ymin,ymax (A): -26.74300 10.72500 zmin,zma (A): -16.37400 36.55300 x,y,z range (A): 44.21500 37.46800 52.92700 scale (grids/A): 2.017874 object centre (A): 1.547501 -8.009001 10.08950 number of atom coordinates read : 2056 total number of charged atoms : 1922 net assigned charge : 6.931010 assigned positive charge : 312.1291 centred at (gu) : 90.45288 92.53086 90.44465 assigned negative charge : -305.1981 centred at (gu) : 89.93478 92.46985 90.42129 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16896 grid for indexing accessible points = 1.400000 m= 25344 mr = 47239 m= 4311 mr = 19018 m= 293 mr = 2714 m= 5 mr = 124 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 0.3400000 number of dielectric boundary points 27528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 15163 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) : 0.6726245 object centre at (A) : 1.547501 -8.009001 10.08950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7715148E-02 3.5866048E-02 midg,1,midg; midg,igrid,midg 5.1907091E-03 2.4667509E-02 1,midg,midg; igrid,midg,midg -2.3337577E-03 3.4050230E-02 gauss-seidel spectral radius is 0.9987157 estimated iterations to convergence 221 setup time was (sec) 0.5600000 now iterating at: 06:39:34 rms-change max change #iterations 4.143268 186.6853 at 10iterations 1.988941 72.07892 at 20iterations 0.9549538 32.63766 at 30iterations 0.4575398 15.53306 at 40iterations 0.2204498 7.025985 at 50iterations 0.1057299 3.314288 at 60iterations 5.1008824E-02 1.578554 at 70iterations 2.4454409E-02 0.8139629 at 80iterations 1.1857493E-02 0.3928108 at 90iterations 5.7466915E-03 0.1875381 at 100iterations 2.8072335E-03 9.1304779E-02 at 110iterations 1.3910284E-03 4.6123505E-02 at 120iterations finished qdiffx linear iterations at : 06:39:41 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.3910284E-03 4.6123505E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 06:39:42 7.688u 0.182s 0:08.18 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 Tue Oct 11 2011 at 06:39:42 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.026810 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): -20.56000 23.65500 ymin,ymax (A): -26.74300 10.72500 zmin,zma (A): -16.37400 36.55300 x,y,z range (A): 44.21500 37.46800 52.92700 scale (grids/A): 3.026810 object centre (A): 1.547501 -8.009001 10.08950 number of atom coordinates read : 2056 total number of charged atoms : 1922 net assigned charge : 6.931010 assigned positive charge : 312.1291 centred at (gu) : 90.67935 93.79630 90.66692 assigned negative charge : -305.1981 centred at (gu) : 89.90226 93.70480 90.63203 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 153966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16896 grid for indexing accessible points = 1.400000 m= 80751 mr = 114206 m= 30477 mr = 66832 m= 8052 mr = 24528 m= 1319 mr = 6044 m= 80 mr = 930 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 62068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 15376 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) : 2.017874 object centre at (A) : 1.547501 -8.009001 10.08950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9123062 0.3281037 midg,1,midg; midg,igrid,midg 3.7097752E-02 0.2086532 1,midg,midg; igrid,midg,midg 2.0963592E-02 0.2789502 gauss-seidel spectral radius is 0.9992636 estimated iterations to convergence 291 setup time was (sec) 1.090000 now iterating at: 06:39:43 rms-change max change #iterations 9.570102 336.0168 at 10iterations 5.598660 122.0168 at 20iterations 3.274493 94.27728 at 30iterations 1.908032 38.70792 at 40iterations 1.110857 29.61975 at 50iterations 0.6430522 13.37370 at 60iterations 0.3740265 7.672486 at 70iterations 0.2168695 4.583721 at 80iterations 0.1253175 2.470575 at 90iterations 7.2707906E-02 1.391144 at 100iterations 4.2237870E-02 0.8942490 at 110iterations 2.4591722E-02 0.4348660 at 120iterations 1.4397585E-02 0.3005314 at 130iterations 8.5629681E-03 0.1612644 at 140iterations 5.1722857E-03 0.1109982 at 150iterations 3.2371576E-03 6.8325043E-02 at 160iterations 2.1243184E-03 4.0481567E-02 at 170iterations 1.4614430E-03 2.7122498E-02 at 180iterations finished qdiffx linear iterations at : 06:39:54 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 1.4614430E-03 2.7122498E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 06:39:55 12.315u 0.216s 0:12.89 97.1% 0+0k 0+0io 0pf+0w