Wed Feb 15 08:56:48 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:49 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1098 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3280 !!! WARNING: HIZ 617 has a net charge of 0.1000 !!! WARNING: HIZ 653 has a net charge of 0.1000 !!! WARNING: DID 654 has a net charge of -0.7500 !!! WARNING: DIC 764 has a net charge of -0.8500 !!! WARNING: ZN 900 has a net charge of 1.4000 !!! WARNING: MG 901 has a net charge of 1.4000 !!! WARNING: WAM 929 has a net charge of 0.1000 !!! WARNING: WAM 972 has a net charge of 0.1000 !!! WARNING: WAM 973 has a net charge of 0.1000 !!! WARNING: WAM 976 has a net charge of 0.1000 !!! WARNING: WAM 977 has a net charge of 0.1000 !!! WARNING: WAM 978 has a net charge of 0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5834535 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): -35.87700 25.13900 ymin,ymax (A): 23.41300 82.67400 zmin,zma (A): 60.42700 108.5950 x,y,z range (A): 61.01600 59.26099 48.16800 scale (grids/A): 0.5834535 object centre (A): -5.369001 53.04350 84.51100 number of atom coordinates read : 3280 total number of charged atoms : 3135 net assigned charge : 2.000008 assigned positive charge : 511.5374 centred at (gu) : 88.64401 91.80612 89.87611 assigned negative charge : -509.5392 centred at (gu) : 88.58897 91.91483 89.87779 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6959 nv = 96 ne = 84 npr = 67522 no. pairs analyzed = 67522 no. exposed pairs = 4089 no. arc points = 28280 no. surface atoms = 1375 nbur = 1905 mkacc time = 0.1500000 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 = 1.484000 m= 332 mr = 3602 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2911 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9109 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4214117E-10 5.1529242E-10 midg,1,midg; midg,igrid,midg 2.3587217E-09 -3.8982360E-09 1,midg,midg; igrid,midg,midg -1.3657731E-09 1.5420429E-09 gauss-seidel spectral radius is 0.9848517 estimated iterations to convergence 67 setup time was (sec) 0.6400000 now iterating at: 08:56:50 rms-change max change #iterations 0.1060829 15.40882 at 10iterations 8.5256705E-03 1.274628 at 20iterations 7.9612457E-04 0.1408882 at 30iterations 1.2218882E-04 2.2379875E-02 at 40iterations 2.9144005E-05 5.5503845E-03 at 50iterations finished qdiffx linear iterations at : 08:56:52 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 2.9144005E-05 5.5503845E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 08:56:53 3.687u 0.235s 0:04.24 92.2% 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 Wed Feb 15 2012 at 08:56:53 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1098 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3280 !!! WARNING: HIZ 617 has a net charge of 0.1000 !!! WARNING: HIZ 653 has a net charge of 0.1000 !!! WARNING: DID 654 has a net charge of -0.7500 !!! WARNING: DIC 764 has a net charge of -0.8500 !!! WARNING: ZN 900 has a net charge of 1.4000 !!! WARNING: MG 901 has a net charge of 1.4000 !!! WARNING: WAM 929 has a net charge of 0.1000 !!! WARNING: WAM 972 has a net charge of 0.1000 !!! WARNING: WAM 973 has a net charge of 0.1000 !!! WARNING: WAM 976 has a net charge of 0.1000 !!! WARNING: WAM 977 has a net charge of 0.1000 !!! WARNING: WAM 978 has a net charge of 0.1000 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: 1.750360 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): -35.87700 25.13900 ymin,ymax (A): 23.41300 82.67400 zmin,zma (A): 60.42700 108.5950 x,y,z range (A): 61.01600 59.26099 48.16800 scale (grids/A): 1.750360 object centre (A): -5.369001 53.04350 84.51100 number of atom coordinates read : 3280 total number of charged atoms : 3135 net assigned charge : 2.000008 assigned positive charge : 511.5374 centred at (gu) : 85.93098 95.41756 89.62703 assigned negative charge : -509.5392 centred at (gu) : 85.76654 95.74431 89.63305 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28280 grid for indexing accessible points = 1.400000 m= 25239 mr = 52017 m= 3554 mr = 17672 m= 166 mr = 1965 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 470 time to turn everything in is 0.6300000 number of dielectric boundary points 33804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 24338 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) : 0.5834535 object centre at (A) : -5.369001 53.04350 84.51100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0894261E-03 5.0458382E-03 midg,1,midg; midg,igrid,midg 2.0839395E-02 -4.7867266E-03 1,midg,midg; igrid,midg,midg -4.3661922E-02 7.9345629E-03 gauss-seidel spectral radius is 0.9984430 estimated iterations to convergence 201 setup time was (sec) 0.9500000 now iterating at: 08:56:54 rms-change max change #iterations 4.155284 177.7702 at 10iterations 1.841159 63.34263 at 20iterations 0.8192646 26.58443 at 30iterations 0.3645867 11.03974 at 40iterations 0.1614761 5.065477 at 50iterations 7.2031319E-02 2.185907 at 60iterations 3.2140777E-02 1.007847 at 70iterations 1.4267103E-02 0.4878731 at 80iterations 6.3421126E-03 0.2088871 at 90iterations 2.8259791E-03 9.1404319E-02 at 100iterations 1.2668447E-03 3.8818359E-02 at 110iterations 5.6822755E-04 1.8886566E-02 at 120iterations finished qdiffx linear iterations at : 08:57:02 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 5.6822755E-04 1.8886566E-02 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.670000 DelPhi exited at 08:57:02 8.672u 0.274s 0:09.29 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 Wed Feb 15 2012 at 08:57:02 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1098 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3280 !!! WARNING: HIZ 617 has a net charge of 0.1000 !!! WARNING: HIZ 653 has a net charge of 0.1000 !!! WARNING: DID 654 has a net charge of -0.7500 !!! WARNING: DIC 764 has a net charge of -0.8500 !!! WARNING: ZN 900 has a net charge of 1.4000 !!! WARNING: MG 901 has a net charge of 1.4000 !!! WARNING: WAM 929 has a net charge of 0.1000 !!! WARNING: WAM 972 has a net charge of 0.1000 !!! WARNING: WAM 973 has a net charge of 0.1000 !!! WARNING: WAM 976 has a net charge of 0.1000 !!! WARNING: WAM 977 has a net charge of 0.1000 !!! WARNING: WAM 978 has a net charge of 0.1000 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: 2.625541 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): -35.87700 25.13900 ymin,ymax (A): 23.41300 82.67400 zmin,zma (A): 60.42700 108.5950 x,y,z range (A): 61.01600 59.26099 48.16800 scale (grids/A): 2.625541 object centre (A): -5.369001 53.04350 84.51100 number of atom coordinates read : 3280 total number of charged atoms : 3135 net assigned charge : 2.000008 assigned positive charge : 511.5374 centred at (gu) : 83.89630 98.12620 89.44032 assigned negative charge : -509.5392 centred at (gu) : 83.64972 98.61642 89.44947 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 177860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28280 grid for indexing accessible points = 1.400000 m= 84007 mr = 127577 m= 27751 mr = 66612 m= 5796 mr = 21300 m= 651 mr = 4039 m= 21 mr = 365 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8199999 no. cavity mid-points inaccessible to solvent = 1755 time to turn everything in is 1.450000 number of dielectric boundary points 76187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 25070 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) : 1.750360 object centre at (A) : -5.369001 53.04350 84.51100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7729743E-02 5.1280580E-02 midg,1,midg; midg,igrid,midg 0.3296134 -3.3428285E-02 1,midg,midg; igrid,midg,midg -0.5522401 8.9324653E-02 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 1.750000 now iterating at: 08:57:04 rms-change max change #iterations 10.24844 279.0703 at 10iterations 5.861506 134.8142 at 20iterations 3.338472 70.57195 at 30iterations 1.900037 40.67189 at 40iterations 1.075243 22.10628 at 50iterations 0.6105160 12.23821 at 60iterations 0.3449954 7.094191 at 70iterations 0.1956045 3.711651 at 80iterations 0.1105052 2.011296 at 90iterations 6.2404085E-02 1.160380 at 100iterations 3.5241798E-02 0.6170797 at 110iterations 1.9931987E-02 0.3876772 at 120iterations 1.1251064E-02 0.2055321 at 130iterations 6.3526714E-03 0.1192780 at 140iterations 3.5981380E-03 6.5258980E-02 at 150iterations 2.0364218E-03 4.1281462E-02 at 160iterations 1.1560594E-03 2.1123886E-02 at 170iterations 6.5796106E-04 1.1802673E-02 at 180iterations finished qdiffx linear iterations at : 08:57:16 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 6.5796106E-04 1.1802673E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 08:57:17 13.588u 0.264s 0:14.33 96.5% 0+0k 0+0io 0pf+0w