Sat Oct 15 13:55:22 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+sph.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 = amb.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 13:55:22 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: ASP 501 has a net charge of -2.0000 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: 0.5285506 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): -16.49500 46.90400 ymin,ymax (A): -3.971000 45.54500 zmin,zma (A): -27.25700 40.09700 x,y,z range (A): 63.39900 49.51600 67.35400 scale (grids/A): 0.5285506 object centre (A): 15.20450 20.78700 6.420000 number of atom coordinates read : 2620 total number of charged atoms : 2489 net assigned charge : -4.999982 assigned positive charge : 377.6512 centred at (gu) : 90.11308 91.65173 92.19724 assigned negative charge : -382.6514 centred at (gu) : 90.27366 91.71308 92.10493 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4866 nv = 96 ne = 84 npr = 51629 no. pairs analyzed = 51629 no. exposed pairs = 3686 no. arc points = 27465 no. surface atoms = 1233 nbur = 1387 mkacc time = 9.0000004E-02 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 = 1.624000 m= 151 mr = 2153 m= 0 mr = 3 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6375 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4407976E-10 2.0107480E-10 midg,1,midg; midg,igrid,midg 1.2030749E-11 -5.0906784E-10 1,midg,midg; igrid,midg,midg 2.9101666E-10 -6.4681360E-10 gauss-seidel spectral radius is 0.9815461 estimated iterations to convergence 61 setup time was (sec) 0.4100000 now iterating at: 13:55:23 rms-change max change #iterations 6.1167490E-02 11.23976 at 10iterations 3.6084284E-03 0.6214581 at 20iterations 2.1928111E-04 4.4543266E-02 at 30iterations 1.3018234E-05 2.4051666E-03 at 40iterations 8.5527756E-07 2.2029877E-04 at 50iterations finished qdiffx linear iterations at : 13:55:26 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 8.5527756E-07 2.2029877E-04 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 13:55:26 3.640u 0.191s 0:04.13 92.7% 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 Sat Oct 15 2011 at 13:55:26 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: ASP 501 has a net charge of -2.0000 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: 1.585652 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): -16.49500 46.90400 ymin,ymax (A): -3.971000 45.54500 zmin,zma (A): -27.25700 40.09700 x,y,z range (A): 63.39900 49.51600 67.35400 scale (grids/A): 1.585652 object centre (A): 15.20450 20.78700 6.420000 number of atom coordinates read : 2620 total number of charged atoms : 2489 net assigned charge : -4.999982 assigned positive charge : 377.6512 centred at (gu) : 90.33906 94.95473 96.59137 assigned negative charge : -382.6514 centred at (gu) : 90.82096 95.13922 96.31443 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 53732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27465 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 13435 mr = 33114 m= 1021 mr = 8137 m= 18 mr = 376 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1225 time to turn everything in is 0.2800000 number of dielectric boundary points 26578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 18969 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) : 0.5285506 object centre at (A) : 15.20450 20.78700 6.420000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2414483E-02 4.4426676E-03 midg,1,midg; midg,igrid,midg -7.7367708E-04 -8.9559546E-03 1,midg,midg; igrid,midg,midg 1.3175659E-02 -1.3317476E-02 gauss-seidel spectral radius is 0.9980451 estimated iterations to convergence 180 setup time was (sec) 0.5100000 now iterating at: 13:55:27 rms-change max change #iterations 2.837444 148.2126 at 10iterations 1.138616 54.59680 at 20iterations 0.4555237 21.81859 at 30iterations 0.1828213 7.769023 at 40iterations 7.3677644E-02 3.524173 at 50iterations 2.9424282E-02 1.194815 at 60iterations 1.1883222E-02 0.5087852 at 70iterations 4.7927527E-03 0.2162762 at 80iterations 1.9301859E-03 8.4201813E-02 at 90iterations 7.7743607E-04 3.3788204E-02 at 100iterations 3.1240020E-04 1.3633728E-02 at 110iterations 1.2593059E-04 5.2957535E-03 at 120iterations finished qdiffx linear iterations at : 13:55:35 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.2593059E-04 5.2957535E-03 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 13:55:35 8.100u 0.223s 0:08.62 96.5% 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 Sat Oct 15 2011 at 13:55:35 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: ASP 501 has a net charge of -2.0000 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: 2.378478 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): -16.49500 46.90400 ymin,ymax (A): -3.971000 45.54500 zmin,zma (A): -27.25700 40.09700 x,y,z range (A): 63.39900 49.51600 67.35400 scale (grids/A): 2.378478 object centre (A): 15.20450 20.78700 6.420000 number of atom coordinates read : 2620 total number of charged atoms : 2489 net assigned charge : -4.999982 assigned positive charge : 377.6512 centred at (gu) : 90.50840 97.43206 99.88692 assigned negative charge : -382.6514 centred at (gu) : 91.23135 97.70867 99.47168 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 125282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27465 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 48995 mr = 82426 m= 10986 mr = 36132 m= 1453 mr = 7359 m= 74 mr = 833 m= 0 mr = 40 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 4102 time to turn everything in is 0.6300000 number of dielectric boundary points 60000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19869 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) : 1.585652 object centre at (A) : 15.20450 20.78700 6.420000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4567672 -2.4363166E-02 midg,1,midg; midg,igrid,midg -2.8736298E-03 -0.1286803 1,midg,midg; igrid,midg,midg 0.1629795 -0.2434933 gauss-seidel spectral radius is 0.9990891 estimated iterations to convergence 262 setup time was (sec) 0.8700000 now iterating at: 13:55:36 rms-change max change #iterations 7.525179 256.9903 at 10iterations 4.163731 127.7573 at 20iterations 2.292462 63.79550 at 30iterations 1.249506 33.11493 at 40iterations 0.6816283 16.98528 at 50iterations 0.3700840 8.957296 at 60iterations 0.2004620 5.271670 at 70iterations 0.1086458 2.659004 at 80iterations 5.8584347E-02 1.375717 at 90iterations 3.1608611E-02 0.7362061 at 100iterations 1.7150333E-02 0.3925008 at 110iterations 9.2562055E-03 0.2324977 at 120iterations 4.9823485E-03 0.1050797 at 130iterations 2.6925018E-03 6.0623169E-02 at 140iterations 1.4501656E-03 3.4255981E-02 at 150iterations 7.7982823E-04 1.6243935E-02 at 160iterations 4.2230205E-04 9.8533630E-03 at 170iterations 2.2756998E-04 4.8904419E-03 at 180iterations finished qdiffx linear iterations at : 13:55:59 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 2.2756998E-04 4.8904419E-03 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 13:56:00 12.478u 0.244s 0:24.38 52.1% 0+0k 0+0io 0pf+0w