Sun Oct 9 14:13:13 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 14:13:13 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 !!! WARNING: HIQ 41 has a net charge of 0.5140 !!! WARNING: SEP 183 has a net charge of -0.4750 !!! WARNING: GLM 210 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: 0.6374674 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 0.6374674 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2324 net assigned charge : 7.945016 assigned positive charge : 372.3171 centred at (gu) : 89.35317 91.00751 90.14434 assigned negative charge : -364.3728 centred at (gu) : 89.29058 90.92506 89.99302 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6710 nv = 96 ne = 84 npr = 50355 no. pairs analyzed = 50355 no. exposed pairs = 3030 no. arc points = 21178 no. surface atoms = 1023 nbur = 1443 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3671 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2166 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8077 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8499107E-09 2.6692824E-08 midg,1,midg; midg,igrid,midg 1.8607234E-09 2.3598137E-08 1,midg,midg; igrid,midg,midg 4.8036526E-09 1.4860018E-08 gauss-seidel spectral radius is 0.9872384 estimated iterations to convergence 72 setup time was (sec) 0.4900000 now iterating at: 14:13:14 rms-change max change #iterations 0.1407168 20.34429 at 10iterations 1.3722913E-02 1.942806 at 20iterations 1.3382566E-03 0.2084703 at 30iterations 1.3291805E-04 1.7969131E-02 at 40iterations 1.2955250E-05 1.7585754E-03 at 50iterations finished qdiffx linear iterations at : 14:13:16 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.2955250E-05 1.7585754E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 14:13:17 3.091u 0.148s 0:03.53 91.5% 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 Sun Oct 9 2011 at 14:13:17 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 !!! WARNING: HIQ 41 has a net charge of 0.5140 !!! WARNING: SEP 183 has a net charge of -0.4750 !!! WARNING: GLM 210 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: 1.912402 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 1.912402 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2324 net assigned charge : 7.945016 assigned positive charge : 372.3171 centred at (gu) : 88.05891 93.02212 90.43260 assigned negative charge : -364.3728 centred at (gu) : 87.87167 92.77504 89.97887 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21178 grid for indexing accessible points = 1.400000 m= 25599 mr = 50429 m= 3563 mr = 18348 m= 175 mr = 1942 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 357 time to turn everything in is 0.5300000 number of dielectric boundary points 31195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18265 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) : 0.6374674 object centre at (A) : 20.66450 33.49400 37.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0168103E-02 6.4736344E-02 midg,1,midg; midg,igrid,midg -1.6922519E-02 7.9215979E-03 1,midg,midg; igrid,midg,midg 2.9545045E-02 4.0501658E-02 gauss-seidel spectral radius is 0.9986348 estimated iterations to convergence 214 setup time was (sec) 0.7900000 now iterating at: 14:13:18 rms-change max change #iterations 4.154630 171.0268 at 10iterations 1.937917 71.71636 at 20iterations 0.9065171 30.94130 at 30iterations 0.4247609 15.39038 at 40iterations 0.1993901 6.973143 at 50iterations 9.3090869E-02 3.040764 at 60iterations 4.3744314E-02 1.356106 at 70iterations 2.0412028E-02 0.6244569 at 80iterations 9.5940745E-03 0.3115969 at 90iterations 4.4985814E-03 0.1397972 at 100iterations 2.1112545E-03 6.6047668E-02 at 110iterations 9.8962220E-04 3.2070160E-02 at 120iterations finished qdiffx linear iterations at : 14:13:24 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 9.8962220E-04 3.2070160E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 14:13:25 7.439u 0.144s 0:07.90 95.8% 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 14:13:25 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 !!! WARNING: HIQ 41 has a net charge of 0.5140 !!! WARNING: SEP 183 has a net charge of -0.4750 !!! WARNING: GLM 210 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.868603 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 2.868603 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2324 net assigned charge : 7.945016 assigned positive charge : 372.3171 centred at (gu) : 87.08817 94.53300 90.64883 assigned negative charge : -364.3728 centred at (gu) : 86.80750 94.16247 89.96832 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 168043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21178 grid for indexing accessible points = 1.400000 m= 83818 mr = 122530 m= 28621 mr = 67900 m= 6143 mr = 22212 m= 727 mr = 4230 m= 38 mr = 355 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 1182 time to turn everything in is 1.290000 number of dielectric boundary points 70158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 18586 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) : 1.912402 object centre at (A) : 20.66450 33.49400 37.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4586346E-02 0.5878063 midg,1,midg; midg,igrid,midg -0.1497331 6.3799970E-02 1,midg,midg; igrid,midg,midg 0.3056442 0.4737821 gauss-seidel spectral radius is 0.9992554 estimated iterations to convergence 289 setup time was (sec) 1.560000 now iterating at: 14:13:26 rms-change max change #iterations 9.830256 513.1777 at 10iterations 5.758988 175.5236 at 20iterations 3.361763 66.09576 at 30iterations 1.958710 37.36452 at 40iterations 1.134159 21.78730 at 50iterations 0.6570714 11.83350 at 60iterations 0.3791312 7.818538 at 70iterations 0.2186223 4.148407 at 80iterations 0.1263963 2.317352 at 90iterations 7.2704352E-02 1.380127 at 100iterations 4.1871343E-02 0.7908497 at 110iterations 2.4033029E-02 0.4514771 at 120iterations 1.3833478E-02 0.2825775 at 130iterations 7.9414835E-03 0.1564941 at 140iterations 4.5668287E-03 9.1698647E-02 at 150iterations 2.6219483E-03 5.0140381E-02 at 160iterations 1.5074537E-03 3.1077385E-02 at 170iterations 8.6685619E-04 1.7009735E-02 at 180iterations finished qdiffx linear iterations at : 14:13:36 total time elapsed so far: 10.82000 # loops : 180 mean,max change (kT/e) : 8.6685619E-04 1.7009735E-02 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.01000 DelPhi exited at 14:13:36 11.014u 0.176s 0:11.46 97.5% 0+0k 0+0io 0pf+0w