Sat Oct 15 15:00:03 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 Sat Oct 15 2011 at 15:00:03 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 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: 0.6327764 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): 5.400000 60.17700 ymin,ymax (A): 7.645999 55.84300 zmin,zma (A): 6.185000 62.44500 x,y,z range (A): 54.77700 48.19700 56.26000 scale (grids/A): 0.6327764 object centre (A): 32.78850 31.74450 34.31500 number of atom coordinates read : 2488 total number of charged atoms : 2354 net assigned charge : 1.000027 assigned positive charge : 369.2930 centred at (gu) : 88.54092 89.47810 90.36754 assigned negative charge : -368.2939 centred at (gu) : 88.44958 89.52315 90.21901 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6792 nv = 96 ne = 84 npr = 49877 no. pairs analyzed = 49877 no. exposed pairs = 3312 no. arc points = 23713 no. surface atoms = 1116 nbur = 1372 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 3503 m= 5 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3100000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2284 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1443771E-08 1.5689539E-08 midg,1,midg; midg,igrid,midg 5.9464469E-09 -2.5328224E-09 1,midg,midg; igrid,midg,midg -9.8537791E-09 6.8712969E-09 gauss-seidel spectral radius is 0.9870635 estimated iterations to convergence 72 setup time was (sec) 0.6600000 now iterating at: 15:00:04 rms-change max change #iterations 0.1388356 27.02756 at 10iterations 1.3268183E-02 1.936989 at 20iterations 1.3138641E-03 0.1867156 at 30iterations 1.3201812E-04 1.8772125E-02 at 40iterations 1.3772412E-05 2.3231506E-03 at 50iterations finished qdiffx linear iterations at : 15:00:11 total time elapsed so far: 5.490000 # loops : 50 mean,max change (kT/e) : 1.3772412E-05 2.3231506E-03 energy calculations done at 5.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.660000 DelPhi exited at 15:00:13 5.663u 0.451s 0:09.49 64.3% 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 Sat Oct 15 2011 at 15:00:13 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 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: 1.898329 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): 5.400000 60.17700 ymin,ymax (A): 7.645999 55.84300 zmin,zma (A): 6.185000 62.44500 x,y,z range (A): 54.77700 48.19700 56.26000 scale (grids/A): 1.898329 object centre (A): 32.78850 31.74450 34.31500 number of atom coordinates read : 2488 total number of charged atoms : 2354 net assigned charge : 1.000027 assigned positive charge : 369.2930 centred at (gu) : 85.62225 88.43372 91.10174 assigned negative charge : -368.2939 centred at (gu) : 85.34874 88.56933 90.65700 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23713 grid for indexing accessible points = 1.400000 m= 25371 mr = 49002 m= 4197 mr = 17899 m= 238 mr = 2539 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33661 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18500 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) : 0.6327764 object centre at (A) : 32.78850 31.74450 34.31500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6115873E-02 1.3687102E-03 midg,1,midg; midg,igrid,midg 1.1292152E-02 -8.8251161E-04 1,midg,midg; igrid,midg,midg 4.8956610E-03 3.8372342E-02 gauss-seidel spectral radius is 0.9986315 estimated iterations to convergence 214 setup time was (sec) 1.030000 now iterating at: 15:00:15 rms-change max change #iterations 4.120893 181.9962 at 10iterations 1.924131 65.80458 at 20iterations 0.8961348 32.88300 at 30iterations 0.4176418 14.22867 at 40iterations 0.1955486 7.617510 at 50iterations 9.1560543E-02 2.822087 at 60iterations 4.2564560E-02 1.331776 at 70iterations 1.9981580E-02 0.5862007 at 80iterations 9.3686823E-03 0.3075600 at 90iterations 4.3740184E-03 0.1377177 at 100iterations 2.0504356E-03 6.9067478E-02 at 110iterations 9.6053764E-04 3.0715942E-02 at 120iterations finished qdiffx linear iterations at : 15:00:31 total time elapsed so far: 14.25000 # loops : 120 mean,max change (kT/e) : 9.6053764E-04 3.0715942E-02 energy calculations done at 14.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.41000 DelPhi exited at 15:00:32 14.417u 0.565s 0:18.80 79.6% 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 15 2011 at 15:00:32 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 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: 2.847494 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): 5.400000 60.17700 ymin,ymax (A): 7.645999 55.84300 zmin,zma (A): 6.185000 62.44500 x,y,z range (A): 54.77700 48.19700 56.26000 scale (grids/A): 2.847494 object centre (A): 32.78850 31.74450 34.31500 number of atom coordinates read : 2488 total number of charged atoms : 2354 net assigned charge : 1.000027 assigned positive charge : 369.2930 centred at (gu) : 83.43333 87.65034 91.65237 assigned negative charge : -368.2939 centred at (gu) : 83.02298 87.85395 90.98551 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 169583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23713 grid for indexing accessible points = 1.400000 m= 81558 mr = 119476 m= 29668 mr = 64834 m= 7447 mr = 23028 m= 989 mr = 5438 m= 49 mr = 573 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 75931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 18832 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) : 1.898329 object centre at (A) : 32.78850 31.74450 34.31500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8995804 4.2851821E-02 midg,1,midg; midg,igrid,midg 0.1066125 -3.7015241E-02 1,midg,midg; igrid,midg,midg 0.2386458 0.5667691 gauss-seidel spectral radius is 0.9992671 estimated iterations to convergence 292 setup time was (sec) 2.310000 now iterating at: 15:00:34 rms-change max change #iterations 9.791628 385.4417 at 10iterations 5.722530 144.7431 at 20iterations 3.328145 67.88039 at 30iterations 1.930232 39.83624 at 40iterations 1.117785 24.48539 at 50iterations 0.6451159 12.34579 at 60iterations 0.3737162 7.007070 at 70iterations 0.2160520 3.900132 at 80iterations 0.1244288 2.334816 at 90iterations 7.1722887E-02 1.331544 at 100iterations 4.1429162E-02 0.7341614 at 110iterations 2.3854850E-02 0.4663773 at 120iterations 1.3742045E-02 0.2505522 at 130iterations 7.9200268E-03 0.1564922 at 140iterations 4.5702839E-03 9.1749191E-02 at 150iterations 2.6375046E-03 5.6200027E-02 at 160iterations 1.5194806E-03 2.8860092E-02 at 170iterations 8.7934732E-04 1.7120361E-02 at 180iterations finished qdiffx linear iterations at : 15:00:56 total time elapsed so far: 23.90000 # loops : 180 mean,max change (kT/e) : 8.7934732E-04 1.7120361E-02 energy calculations done at 23.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.06000 DelPhi exited at 15:00:57 24.066u 0.528s 0:25.13 97.8% 0+0k 0+0io 0pf+0w