Sat Oct 8 20:31:16 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 8 2011 at 20:31:16 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 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: 0.6161515 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): -30.81900 17.32300 ymin,ymax (A): -23.62500 23.63500 zmin,zma (A): -12.59300 45.18500 x,y,z range (A): 48.14200 47.26000 57.77800 scale (grids/A): 0.6161515 object centre (A): -6.748000 5.0001144E-03 16.29600 number of atom coordinates read : 2593 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.41330 89.01820 89.70598 assigned negative charge : -387.4045 centred at (gu) : 88.32375 89.06079 89.58199 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6350 nv = 96 ne = 84 npr = 54589 no. pairs analyzed = 54589 no. exposed pairs = 2989 no. arc points = 21491 no. surface atoms = 1005 nbur = 1588 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3555 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.2000000 number of dielectric boundary points 3109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2149 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7968 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7961777E-09 9.5279145E-09 midg,1,midg; midg,igrid,midg 6.7732908E-09 3.6500059E-10 1,midg,midg; igrid,midg,midg -3.5157366E-09 5.7774505E-09 gauss-seidel spectral radius is 0.9863546 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 20:31:16 rms-change max change #iterations 0.1224710 21.39035 at 10iterations 1.1045546E-02 1.614121 at 20iterations 1.0015431E-03 0.1529236 at 30iterations 9.8358549E-05 1.4251709E-02 at 40iterations 9.6129943E-06 1.4286041E-03 at 50iterations finished qdiffx linear iterations at : 20:31:19 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 9.6129943E-06 1.4286041E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 20:31:19 3.391u 0.162s 0:03.83 92.6% 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 8 2011 at 20:31:19 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 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: 1.848454 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): -30.81900 17.32300 ymin,ymax (A): -23.62500 23.63500 zmin,zma (A): -12.59300 45.18500 x,y,z range (A): 48.14200 47.26000 57.77800 scale (grids/A): 1.848454 object centre (A): -6.748000 5.0001144E-03 16.29600 number of atom coordinates read : 2593 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.23954 87.05421 89.11752 assigned negative charge : -387.4045 centred at (gu) : 84.97122 87.18196 88.74593 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69720 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21491 grid for indexing accessible points = 1.400000 m= 23620 mr = 48915 m= 3221 mr = 17303 m= 113 mr = 1859 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2968 time to turn everything in is 0.3400000 number of dielectric boundary points 28577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19251 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) : 0.6161515 object centre at (A) : -6.748000 5.0001144E-03 16.29600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9769290E-02 2.4367522E-02 midg,1,midg; midg,igrid,midg 1.2934075E-02 6.0227438E-04 1,midg,midg; igrid,midg,midg -1.2173933E-03 2.7825385E-02 gauss-seidel spectral radius is 0.9985464 estimated iterations to convergence 208 setup time was (sec) 0.5600000 now iterating at: 20:31:20 rms-change max change #iterations 3.955274 163.8212 at 10iterations 1.814799 62.62488 at 20iterations 0.8243057 30.85506 at 30iterations 0.3767498 13.03704 at 40iterations 0.1729757 5.943817 at 50iterations 7.9069674E-02 2.752391 at 60iterations 3.6189720E-02 1.109715 at 70iterations 1.6497249E-02 0.5378170 at 80iterations 7.5528962E-03 0.2438469 at 90iterations 3.4497641E-03 0.1065769 at 100iterations 1.5807634E-03 5.8731079E-02 at 110iterations 7.2618818E-04 2.3624420E-02 at 120iterations finished qdiffx linear iterations at : 20:31:27 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 7.2618818E-04 2.3624420E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 20:31:28 7.784u 0.202s 0:08.26 96.6% 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 8 2011 at 20:31:28 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 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: 2.772682 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): -30.81900 17.32300 ymin,ymax (A): -23.62500 23.63500 zmin,zma (A): -12.59300 45.18500 x,y,z range (A): 48.14200 47.26000 57.77800 scale (grids/A): 2.772682 object centre (A): -6.748000 5.0001144E-03 16.29600 number of atom coordinates read : 2593 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.85920 85.58132 88.67625 assigned negative charge : -387.4045 centred at (gu) : 82.45686 85.77298 88.11891 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21491 grid for indexing accessible points = 1.400000 m= 78645 mr = 118468 m= 26018 mr = 64470 m= 5433 mr = 20726 m= 518 mr = 3938 m= 20 mr = 287 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 9894 time to turn everything in is 0.8600000 number of dielectric boundary points 64406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 19630 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) : 1.848454 object centre at (A) : -6.748000 5.0001144E-03 16.29600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1137846 0.2713937 midg,1,midg; midg,igrid,midg 0.1440319 -1.5180079E-02 1,midg,midg; igrid,midg,midg 6.8438249E-03 0.3648258 gauss-seidel spectral radius is 0.9992280 estimated iterations to convergence 284 setup time was (sec) 1.100000 now iterating at: 20:31:29 rms-change max change #iterations 9.363158 302.2129 at 10iterations 5.375078 128.3225 at 20iterations 3.064822 62.89223 at 30iterations 1.747637 38.08706 at 40iterations 0.9948006 19.92792 at 50iterations 0.5661216 12.58747 at 60iterations 0.3216106 6.741171 at 70iterations 0.1826987 3.536148 at 80iterations 0.1036949 2.084685 at 90iterations 5.8865726E-02 1.115925 at 100iterations 3.3423480E-02 0.7109737 at 110iterations 1.8970862E-02 0.3509789 at 120iterations 1.0785784E-02 0.2003632 at 130iterations 6.1212629E-03 0.1144409 at 140iterations 3.4785524E-03 6.4976692E-02 at 150iterations 1.9775555E-03 3.5679698E-02 at 160iterations 1.1281053E-03 2.2399902E-02 at 170iterations 6.4195722E-04 1.3153076E-02 at 180iterations finished qdiffx linear iterations at : 20:31:40 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 6.4195722E-04 1.3153076E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 20:31:41 12.527u 0.209s 0:13.01 97.7% 0+0k 0+0io 0pf+0w