Tue Oct 11 00:36:52 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 00:36:52 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: GLM 262 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6238062 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): 13.26600 70.33500 ymin,ymax (A): -11.41500 44.31200 zmin,zma (A): 34.58500 77.14000 x,y,z range (A): 57.06900 55.72700 42.55500 scale (grids/A): 0.6238062 object centre (A): 41.80050 16.44850 55.86250 number of atom coordinates read : 2637 total number of charged atoms : 2489 net assigned charge : 3.406016 assigned positive charge : 396.4178 centred at (gu) : 91.48150 89.73749 90.14697 assigned negative charge : -393.0124 centred at (gu) : 91.22211 89.91240 89.93484 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6786 nv = 96 ne = 84 npr = 53981 no. pairs analyzed = 53981 no. exposed pairs = 3049 no. arc points = 21473 no. surface atoms = 1030 nbur = 1607 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3898 m= 0 mr = 33 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.3400000 number of dielectric boundary points 3200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2096 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3116839E-08 1.8895266E-08 midg,1,midg; midg,igrid,midg 1.6549013E-08 -1.0028814E-08 1,midg,midg; igrid,midg,midg -1.2416251E-08 3.0154009E-08 gauss-seidel spectral radius is 0.9866906 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 00:36:53 rms-change max change #iterations 0.1340621 19.94022 at 10iterations 1.2962867E-02 2.014984 at 20iterations 1.4374912E-03 0.2962456 at 30iterations 2.3176134E-04 5.0144196E-02 at 40iterations 4.6226854E-05 1.1089325E-02 at 50iterations finished qdiffx linear iterations at : 00:36:56 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 4.6226854E-05 1.1089325E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 00:36:57 4.145u 0.265s 0:04.92 89.4% 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 Tue Oct 11 2011 at 00:36:57 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: GLM 262 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.871419 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): 13.26600 70.33500 ymin,ymax (A): -11.41500 44.31200 zmin,zma (A): 34.58500 77.14000 x,y,z range (A): 57.06900 55.72700 42.55500 scale (grids/A): 1.871419 object centre (A): 41.80050 16.44850 55.86250 number of atom coordinates read : 2637 total number of charged atoms : 2489 net assigned charge : 3.406016 assigned positive charge : 396.4178 centred at (gu) : 94.44394 89.21184 90.44016 assigned negative charge : -393.0124 centred at (gu) : 93.66607 89.73695 89.80436 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21473 grid for indexing accessible points = 1.400000 m= 26427 mr = 52808 m= 3718 mr = 19773 m= 140 mr = 2366 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 3883 time to turn everything in is 0.6400000 number of dielectric boundary points 29476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 19563 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) : 0.6238062 object centre at (A) : 41.80050 16.44850 55.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1549782E-04 3.3347219E-02 midg,1,midg; midg,igrid,midg 4.2338565E-02 -2.7798602E-02 1,midg,midg; igrid,midg,midg -6.0608372E-02 -1.4198751E-02 gauss-seidel spectral radius is 0.9985873 estimated iterations to convergence 211 setup time was (sec) 0.9500000 now iterating at: 00:36:58 rms-change max change #iterations 4.132942 172.9848 at 10iterations 1.903401 66.09814 at 20iterations 0.8781453 30.90495 at 30iterations 0.4080761 13.15703 at 40iterations 0.1889094 6.088196 at 50iterations 8.7407924E-02 2.701513 at 60iterations 4.0543959E-02 1.373417 at 70iterations 1.8818505E-02 0.6277008 at 80iterations 8.7795490E-03 0.2628098 at 90iterations 4.1318974E-03 0.1367474 at 100iterations 1.9713566E-03 7.0999146E-02 at 110iterations 9.7156613E-04 3.6151886E-02 at 120iterations finished qdiffx linear iterations at : 00:37:07 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 9.7156613E-04 3.6151886E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 00:37:07 9.548u 0.313s 0:10.24 96.1% 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 00:37:07 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: GLM 262 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.807128 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): 13.26600 70.33500 ymin,ymax (A): -11.41500 44.31200 zmin,zma (A): 34.58500 77.14000 x,y,z range (A): 57.06900 55.72700 42.55500 scale (grids/A): 2.807128 object centre (A): 41.80050 16.44850 55.86250 number of atom coordinates read : 2637 total number of charged atoms : 2489 net assigned charge : 3.406016 assigned positive charge : 396.4178 centred at (gu) : 96.66588 88.81750 90.66019 assigned negative charge : -393.0124 centred at (gu) : 95.49907 89.60526 89.70639 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 172072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21473 grid for indexing accessible points = 1.400000 m= 86684 mr = 127769 m= 30123 mr = 71929 m= 6453 mr = 24526 m= 711 mr = 4889 m= 27 mr = 453 m= 0 mr = 2 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 13126 time to turn everything in is 1.660000 number of dielectric boundary points 66502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 19908 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) : 1.871419 object centre at (A) : 41.80050 16.44850 55.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6863992E-02 0.3235025 midg,1,midg; midg,igrid,midg 0.5609018 -0.4206500 1,midg,midg; igrid,midg,midg -0.7473018 -0.2173606 gauss-seidel spectral radius is 0.9992410 estimated iterations to convergence 287 setup time was (sec) 1.980000 now iterating at: 00:37:09 rms-change max change #iterations 9.656653 323.2937 at 10iterations 5.545242 126.3147 at 20iterations 3.179924 63.42809 at 30iterations 1.818136 32.93705 at 40iterations 1.038233 18.83585 at 50iterations 0.5917333 11.29507 at 60iterations 0.3379577 6.080229 at 70iterations 0.1925119 4.110423 at 80iterations 0.1096437 2.044067 at 90iterations 6.2802874E-02 1.188576 at 100iterations 3.5864480E-02 0.6238823 at 110iterations 2.0535216E-02 0.3916397 at 120iterations 1.1783355E-02 0.2243118 at 130iterations 6.8121040E-03 0.1272964 at 140iterations 3.9736796E-03 8.1436157E-02 at 150iterations 2.3684578E-03 4.9026489E-02 at 160iterations 1.4457937E-03 3.2699585E-02 at 170iterations 9.2414470E-04 2.2785187E-02 at 180iterations finished qdiffx linear iterations at : 00:37:23 total time elapsed so far: 15.71000 # loops : 180 mean,max change (kT/e) : 9.2414470E-04 2.2785187E-02 energy calculations done at 15.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.90000 DelPhi exited at 00:37:24 15.898u 0.328s 0:16.59 97.7% 0+0k 0+0io 0pf+0w