Sun Oct 9 11:34:51 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 11:34:51 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: CME 1 has a net charge of -0.0350 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: 0.5987923 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): -16.80300 42.30100 ymin,ymax (A): -7.972000 48.22600 zmin,zma (A): -58.59100 0.8620000 x,y,z range (A): 59.10400 56.19800 59.45300 scale (grids/A): 0.5987923 object centre (A): 12.74900 20.12700 -28.86450 number of atom coordinates read : 3122 total number of charged atoms : 3020 net assigned charge : -0.5349858 assigned positive charge : 464.7774 centred at (gu) : 92.00889 91.62582 91.60352 assigned negative charge : -465.3143 centred at (gu) : 91.93801 91.66259 91.54622 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7815 nv = 96 ne = 84 npr = 58810 no. pairs analyzed = 58810 no. exposed pairs = 4561 no. arc points = 33475 no. surface atoms = 1522 nbur = 1600 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 379 mr = 3668 m= 5 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3276 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9631 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8737050E-09 3.0248768E-09 midg,1,midg; midg,igrid,midg 8.4321744E-10 -2.6826399E-09 1,midg,midg; igrid,midg,midg -2.0727811E-09 4.2246131E-09 gauss-seidel spectral radius is 0.9856366 estimated iterations to convergence 68 setup time was (sec) 0.5300000 now iterating at: 11:34:52 rms-change max change #iterations 0.1140964 24.03035 at 10iterations 9.7111044E-03 1.454272 at 20iterations 8.2320400E-04 0.1335602 at 30iterations 6.8719208E-05 9.5148087E-03 at 40iterations 6.0628017E-06 1.1177063E-03 at 50iterations finished qdiffx linear iterations at : 11:34:54 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 6.0628017E-06 1.1177063E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 11:34:55 3.072u 0.157s 0:03.51 91.7% 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 11:34:55 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: CME 1 has a net charge of -0.0350 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: 1.796377 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): -16.80300 42.30100 ymin,ymax (A): -7.972000 48.22600 zmin,zma (A): -58.59100 0.8620000 x,y,z range (A): 59.10400 56.19800 59.45300 scale (grids/A): 1.796377 object centre (A): 12.74900 20.12700 -28.86450 number of atom coordinates read : 3122 total number of charged atoms : 3020 net assigned charge : -0.5349858 assigned positive charge : 464.7774 centred at (gu) : 96.02576 94.87647 94.80954 assigned negative charge : -465.3143 centred at (gu) : 95.81367 94.98750 94.63835 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33475 grid for indexing accessible points = 1.400000 m= 27613 mr = 53352 m= 4074 mr = 18592 m= 155 mr = 2237 m= 0 mr = 21 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 703 time to turn everything in is 0.5800000 number of dielectric boundary points 41742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23546 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) : 0.5987923 object centre at (A) : 12.74900 20.12700 -28.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8773515E-02 1.3000630E-02 midg,1,midg; midg,igrid,midg -1.0088395E-02 -4.9214968E-03 1,midg,midg; igrid,midg,midg 2.8470678E-03 8.9473436E-03 gauss-seidel spectral radius is 0.9985554 estimated iterations to convergence 209 setup time was (sec) 0.8500000 now iterating at: 11:34:56 rms-change max change #iterations 4.208876 182.7360 at 10iterations 1.914862 64.19374 at 20iterations 0.8727837 27.49553 at 30iterations 0.3979324 11.96780 at 40iterations 0.1814755 6.069964 at 50iterations 8.2872391E-02 2.606262 at 60iterations 3.7924532E-02 1.215899 at 70iterations 1.7296700E-02 0.5389442 at 80iterations 7.9144556E-03 0.2608328 at 90iterations 3.6193340E-03 0.1258099 at 100iterations 1.6543193E-03 5.6348801E-02 at 110iterations 7.5726677E-04 2.4028778E-02 at 120iterations finished qdiffx linear iterations at : 11:35:02 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 7.5726677E-04 2.4028778E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 11:35:02 7.040u 0.154s 0:07.47 96.2% 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 11:35:02 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: CME 1 has a net charge of -0.0350 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: 2.694566 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): -16.80300 42.30100 ymin,ymax (A): -7.972000 48.22600 zmin,zma (A): -58.59100 0.8620000 x,y,z range (A): 59.10400 56.19800 59.45300 scale (grids/A): 2.694566 object centre (A): 12.74900 20.12700 -28.86450 number of atom coordinates read : 3122 total number of charged atoms : 3020 net assigned charge : -0.5349858 assigned positive charge : 464.7774 centred at (gu) : 99.03839 97.31441 97.21399 assigned negative charge : -465.3143 centred at (gu) : 98.72052 97.48103 96.95741 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 194520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33475 grid for indexing accessible points = 1.400000 m= 89761 mr = 131316 m= 31130 mr = 69154 m= 7022 mr = 23411 m= 800 mr = 4854 m= 26 mr = 476 m= 0 mr = 3 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 2346 time to turn everything in is 1.380000 number of dielectric boundary points 94045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 24151 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) : 1.796377 object centre at (A) : 12.74900 20.12700 -28.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4804184 0.1374236 midg,1,midg; midg,igrid,midg -0.1795119 -5.8884256E-02 1,midg,midg; igrid,midg,midg 6.8294317E-02 -2.2422967E-02 gauss-seidel spectral radius is 0.9992651 estimated iterations to convergence 291 setup time was (sec) 1.660000 now iterating at: 11:35:04 rms-change max change #iterations 10.45019 306.8744 at 10iterations 6.254097 165.6158 at 20iterations 3.701386 78.29643 at 30iterations 2.167265 46.58390 at 40iterations 1.270485 24.92496 at 50iterations 0.7390738 14.80523 at 60iterations 0.4292160 9.586252 at 70iterations 0.2484237 4.725399 at 80iterations 0.1439976 2.597844 at 90iterations 8.3089732E-02 1.508869 at 100iterations 4.8085101E-02 0.9007049 at 110iterations 2.7769165E-02 0.5150862 at 120iterations 1.6007619E-02 0.2800732 at 130iterations 9.2250053E-03 0.1646099 at 140iterations 5.3253858E-03 9.2197418E-02 at 150iterations 3.0719512E-03 5.7270288E-02 at 160iterations 1.7684408E-03 3.2550514E-02 at 170iterations 1.0196865E-03 1.7243385E-02 at 180iterations finished qdiffx linear iterations at : 11:35:14 total time elapsed so far: 11.29000 # loops : 180 mean,max change (kT/e) : 1.0196865E-03 1.7243385E-02 energy calculations done at 11.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 11:35:14 11.462u 0.168s 0:11.91 97.5% 0+0k 0+0io 0pf+0w