Sat Oct 15 13:21:25 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 13:21:29 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3175 !!! WARNING: SEP 140 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6611816 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): -8.995000 44.84800 ymin,ymax (A): -13.73700 38.90500 zmin,zma (A): 38.00400 90.21900 x,y,z range (A): 53.84300 52.64200 52.21500 scale (grids/A): 0.6611816 object centre (A): 17.92650 12.58400 64.11150 number of atom coordinates read : 3175 total number of charged atoms : 3025 net assigned charge : 4.025008 assigned positive charge : 482.6087 centred at (gu) : 91.09851 90.65247 88.80562 assigned negative charge : -478.5850 centred at (gu) : 91.12454 90.67680 88.89788 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9426 nv = 96 ne = 84 npr = 62806 no. pairs analyzed = 62806 no. exposed pairs = 4195 no. arc points = 29943 no. surface atoms = 1387 nbur = 1788 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 552 mr = 4921 m= 6 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 92 time to turn everything in is 0.3900000 number of dielectric boundary points 4988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2834 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 11046 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2744322E-08 -9.9969943E-09 midg,1,midg; midg,igrid,midg 1.4395843E-08 4.7804858E-09 1,midg,midg; igrid,midg,midg 1.3491803E-08 4.6447304E-09 gauss-seidel spectral radius is 0.9882060 estimated iterations to convergence 75 setup time was (sec) 0.6900000 now iterating at: 13:21:33 rms-change max change #iterations 0.1892749 25.35610 at 10iterations 1.9965418E-02 2.502403 at 20iterations 2.1685711E-03 0.3266182 at 30iterations 2.5054204E-04 3.6483765E-02 at 40iterations 4.1532297E-05 5.1403046E-03 at 50iterations finished qdiffx linear iterations at : 13:21:43 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 4.1532297E-05 5.1403046E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 13:21:45 4.209u 0.272s 0:16.90 26.4% 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 Sat Oct 15 2011 at 13:21:47 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3175 !!! WARNING: SEP 140 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.983545 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): -8.995000 44.84800 ymin,ymax (A): -13.73700 38.90500 zmin,zma (A): 38.00400 90.21900 x,y,z range (A): 53.84300 52.64200 52.21500 scale (grids/A): 1.983545 object centre (A): 17.92650 12.58400 64.11150 number of atom coordinates read : 3175 total number of charged atoms : 3025 net assigned charge : 4.025008 assigned positive charge : 482.6087 centred at (gu) : 93.29477 91.95680 86.41621 assigned negative charge : -478.5850 centred at (gu) : 93.37340 92.03011 86.69324 start vw surface at 0.1800000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 100844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29943 grid for indexing accessible points = 1.400000 m= 36648 mr = 68214 m= 6446 mr = 26312 m= 530 mr = 3940 m= 11 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2727 time to turn everything in is 0.9000000 number of dielectric boundary points 45796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 23918 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) : 0.6611816 object centre at (A) : 17.92650 12.58400 64.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8959706E-02 -7.0846984E-03 midg,1,midg; midg,igrid,midg 8.3366787E-04 -1.3400543E-02 1,midg,midg; igrid,midg,midg 1.5743773E-02 3.6324274E-02 gauss-seidel spectral radius is 0.9988047 estimated iterations to convergence 229 setup time was (sec) 1.210000 now iterating at: 13:21:54 rms-change max change #iterations 5.170630 198.1571 at 10iterations 2.542566 74.27456 at 20iterations 1.248147 34.45002 at 30iterations 0.6128646 17.08411 at 40iterations 0.3014160 8.512794 at 50iterations 0.1478530 4.506100 at 60iterations 7.2673753E-02 2.018861 at 70iterations 3.5868857E-02 1.006287 at 80iterations 1.7580250E-02 0.5016336 at 90iterations 8.6362623E-03 0.2388115 at 100iterations 4.2529637E-03 0.1132326 at 110iterations 2.0962358E-03 5.8498025E-02 at 120iterations finished qdiffx linear iterations at : 13:22:19 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 2.0962358E-03 5.8498025E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.940000 DelPhi exited at 13:22:21 9.942u 0.305s 0:34.16 29.9% 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 13:22:28 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3175 !!! WARNING: SEP 140 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.975317 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): -8.995000 44.84800 ymin,ymax (A): -13.73700 38.90500 zmin,zma (A): 38.00400 90.21900 x,y,z range (A): 53.84300 52.64200 52.21500 scale (grids/A): 2.975317 object centre (A): 17.92650 12.58400 64.11150 number of atom coordinates read : 3175 total number of charged atoms : 3025 net assigned charge : 4.025008 assigned positive charge : 482.6087 centred at (gu) : 94.94186 92.93491 84.62417 assigned negative charge : -478.5850 centred at (gu) : 95.05987 93.04503 85.03998 start vw surface at 0.1700000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 232905 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29943 grid for indexing accessible points = 1.400000 m= 117039 mr = 165435 m= 43672 mr = 94520 m= 11902 mr = 34254 m= 2072 mr = 8722 m= 171 mr = 1428 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 8615 time to turn everything in is 2.320000 number of dielectric boundary points 103332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 24200 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) : 1.983545 object centre at (A) : 17.92650 12.58400 64.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1640045 -2.7395707E-02 midg,1,midg; midg,igrid,midg -2.1624828E-02 -0.3476516 1,midg,midg; igrid,midg,midg 0.1381709 0.1949643 gauss-seidel spectral radius is 0.9993321 estimated iterations to convergence 305 setup time was (sec) 2.680000 now iterating at: 13:22:39 rms-change max change #iterations 12.12822 370.0153 at 10iterations 7.375146 162.0358 at 20iterations 4.462157 94.66348 at 30iterations 2.697236 57.34960 at 40iterations 1.613515 29.77229 at 50iterations 0.9685083 19.30244 at 60iterations 0.5768667 11.36317 at 70iterations 0.3446845 6.220335 at 80iterations 0.2048974 3.197861 at 90iterations 0.1219064 2.015564 at 100iterations 7.2464570E-02 1.251616 at 110iterations 4.3118581E-02 0.7361279 at 120iterations 2.5529696E-02 0.3865271 at 130iterations 1.5189628E-02 0.2773776 at 140iterations 9.0065533E-03 0.1447906 at 150iterations 5.3526876E-03 9.5893234E-02 at 160iterations 3.1714742E-03 5.0362468E-02 at 170iterations 1.8855851E-03 2.8277397E-02 at 180iterations finished qdiffx linear iterations at : 13:23:22 total time elapsed so far: 17.22000 # loops : 180 mean,max change (kT/e) : 1.8855851E-03 2.8277397E-02 energy calculations done at 17.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.40000 DelPhi exited at 13:23:24 17.402u 0.299s 0:56.85 31.1% 0+0k 0+0io 0pf+0w