Tue Nov 8 15:49:37 PST 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 Tue Nov 8 2011 at 15:49:37 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= 7.9999998E-02 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 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6951 nv = 96 ne = 84 npr = 67637 no. pairs analyzed = 67637 no. exposed pairs = 3962 no. arc points = 27530 no. surface atoms = 1336 nbur = 1944 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 = 1.484000 m= 324 mr = 3676 m= 2 mr = 31 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 0.2800000 number of dielectric boundary points 3570 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2861 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.3500000 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 0.9848508 estimated iterations to convergence 67 setup time was (sec) 0.4900000 now iterating at: 15:49:38 rms-change max change #iterations 0.1076082 14.17295 at 10iterations 8.5993251E-03 1.159378 at 20iterations 8.2586496E-04 0.1467590 at 30iterations 1.3263848E-04 2.4261475E-02 at 40iterations 3.1962230E-05 6.1178207E-03 at 50iterations finished qdiffx linear iterations at : 15:49:41 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 3.1962230E-05 6.1178207E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 15:49:49 3.581u 0.185s 0:11.67 32.2% 0+0k 0+46016io 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 Nov 8 2011 at 15:49:49 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= 7.0000000E-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 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 76630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27530 grid for indexing accessible points = 1.400000 m= 25011 mr = 52642 m= 3530 mr = 17700 m= 172 mr = 2007 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 429 time to turn everything in is 0.4900000 number of dielectric boundary points 32964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 iepsmp to db, and charging done at 0.5700000 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 5.7419213E-03 5.1147016E-03 midg,1,midg; midg,igrid,midg 2.0862261E-02 -4.3965252E-03 1,midg,midg; igrid,midg,midg -4.3613348E-02 7.9032155E-03 gauss-seidel spectral radius is 0.9984405 estimated iterations to convergence 201 setup time was (sec) 0.6900000 now iterating at: 15:49:51 rms-change max change #iterations 4.159246 177.6580 at 10iterations 1.841838 63.26454 at 20iterations 0.8203034 26.30827 at 30iterations 0.3648087 11.33097 at 40iterations 0.1614400 5.133484 at 50iterations 7.1960390E-02 2.194544 at 60iterations 3.2145213E-02 1.037554 at 70iterations 1.4251737E-02 0.4869852 at 80iterations 6.3358555E-03 0.1927700 at 90iterations 2.8222515E-03 8.8890076E-02 at 100iterations 1.2664462E-03 4.0092468E-02 at 110iterations 5.7039486E-04 1.8600464E-02 at 120iterations finished qdiffx linear iterations at : 15:49:58 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 5.7039486E-04 1.8600464E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 15:49:59 8.098u 0.212s 0:09.72 85.3% 0+0k 0+45352io 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 Nov 8 2011 at 15:49:59 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= 7.0000000E-02 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 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 178383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27530 grid for indexing accessible points = 1.400000 m= 83701 mr = 129091 m= 27378 mr = 66867 m= 5827 mr = 21166 m= 696 mr = 4152 m= 23 mr = 408 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.7700001 no. cavity mid-points inaccessible to solvent = 1626 time to turn everything in is 1.210000 number of dielectric boundary points 74318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.310000 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 5.3293265E-02 5.2278996E-02 midg,1,midg; midg,igrid,midg 0.3301359 -2.7143095E-02 1,midg,midg; igrid,midg,midg -0.5510567 8.9905173E-02 gauss-seidel spectral radius is 0.9992113 estimated iterations to convergence 281 setup time was (sec) 1.450000 now iterating at: 15:50:09 rms-change max change #iterations 10.20953 278.7028 at 10iterations 5.822084 134.4550 at 20iterations 3.306006 68.76675 at 30iterations 1.877524 38.92046 at 40iterations 1.060044 20.48470 at 50iterations 0.6000163 11.24853 at 60iterations 0.3385181 6.797688 at 70iterations 0.1917192 3.450636 at 80iterations 0.1079685 1.966888 at 90iterations 6.0917739E-02 1.130547 at 100iterations 3.4291517E-02 0.6321602 at 110iterations 1.9363213E-02 0.3402901 at 120iterations 1.0920653E-02 0.1947670 at 130iterations 6.1631948E-03 0.1196432 at 140iterations 3.4935833E-03 6.9168091E-02 at 150iterations 1.9733871E-03 4.0951490E-02 at 160iterations 1.1220477E-03 2.0240784E-02 at 170iterations 6.4068253E-04 1.1548996E-02 at 180iterations finished qdiffx linear iterations at : 15:50:20 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 6.4068253E-04 1.1548996E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 15:50:27 13.064u 0.206s 0:28.33 46.8% 0+0k 0+45352io 0pf+0w