Tue Oct 11 08:34:04 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 Tue Oct 11 2011 at 08:34:04 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 0.7307811 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): 25.60800 72.02600 ymin,ymax (A): -18.75400 29.96100 zmin,zma (A): 3.919000 46.33800 x,y,z range (A): 46.41800 48.71500 42.41900 scale (grids/A): 0.7307811 object centre (A): 48.81700 5.603500 25.12850 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 89.12579 90.55357 90.29761 assigned negative charge : -311.0742 centred at (gu) : 89.25803 90.49966 90.38187 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7730 nv = 96 ne = 84 npr = 41574 no. pairs analyzed = 41574 no. exposed pairs = 2536 no. arc points = 17336 no. surface atoms = 863 nbur = 1418 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 554 mr = 4554 m= 4 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1531 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8212 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5204367E-07 2.4262281E-08 midg,1,midg; midg,igrid,midg 4.3970974E-08 1.5113450E-07 1,midg,midg; igrid,midg,midg 2.3493544E-07 -1.3312776E-08 gauss-seidel spectral radius is 0.9902350 estimated iterations to convergence 82 setup time was (sec) 0.5400000 now iterating at: 08:34:05 rms-change max change #iterations 0.2265614 28.99334 at 10iterations 3.0129939E-02 3.767763 at 20iterations 4.1312785E-03 0.4983215 at 30iterations 6.6681457E-04 9.1270447E-02 at 40iterations 1.6249318E-04 1.9683838E-02 at 50iterations finished qdiffx linear iterations at : 08:34:07 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.6249318E-04 1.9683838E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:34:08 3.383u 0.149s 0:04.07 86.4% 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 08:34:08 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 2.192343 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): 25.60800 72.02600 ymin,ymax (A): -18.75400 29.96100 zmin,zma (A): 3.919000 46.33800 x,y,z range (A): 46.41800 48.71500 42.41900 scale (grids/A): 2.192343 object centre (A): 48.81700 5.603500 25.12850 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 87.37727 91.66052 90.89265 assigned negative charge : -311.0742 centred at (gu) : 87.77424 91.49896 91.14570 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81339 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17336 grid for indexing accessible points = 1.400000 m= 34388 mr = 58457 m= 7196 mr = 26540 m= 742 mr = 5006 m= 30 mr = 411 m= 0 mr = 6 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15581 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) : 0.7307811 object centre at (A) : 48.81700 5.603500 25.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6726680E-02 3.2859616E-02 midg,1,midg; midg,igrid,midg 5.0393622E-02 3.3837289E-02 1,midg,midg; igrid,midg,midg 4.9434379E-02 -5.4938175E-02 gauss-seidel spectral radius is 0.9988965 estimated iterations to convergence 238 setup time was (sec) 0.9400000 now iterating at: 08:34:09 rms-change max change #iterations 4.898129 200.4854 at 10iterations 2.468325 82.78438 at 20iterations 1.252767 39.05925 at 30iterations 0.6330326 17.94135 at 40iterations 0.3197079 8.978142 at 50iterations 0.1624435 5.097645 at 60iterations 8.2437456E-02 2.271689 at 70iterations 4.1833792E-02 1.189934 at 80iterations 2.1228975E-02 0.6639938 at 90iterations 1.0869222E-02 0.3238173 at 100iterations 5.5563380E-03 0.1619000 at 110iterations 2.8980942E-03 8.4426880E-02 at 120iterations finished qdiffx linear iterations at : 08:34:16 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.8980942E-03 8.4426880E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 08:34:17 7.887u 0.211s 0:08.85 91.4% 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 08:34:17 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 3.288515 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): 25.60800 72.02600 ymin,ymax (A): -18.75400 29.96100 zmin,zma (A): 3.919000 46.33800 x,y,z range (A): 46.41800 48.71500 42.41900 scale (grids/A): 3.288515 object centre (A): 48.81700 5.603500 25.12850 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 86.06584 92.49084 91.33900 assigned negative charge : -311.0742 centred at (gu) : 86.66142 92.24849 91.71859 start vw surface at 0.1500000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 187083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17336 grid for indexing accessible points = 1.400000 m= 105275 mr = 139989 m= 45312 mr = 88561 m= 13820 mr = 37863 m= 3039 mr = 10939 m= 408 mr = 2241 m= 34 mr = 279 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.050000 number of dielectric boundary points 75075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 15688 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) : 2.192343 object centre at (A) : 48.81700 5.603500 25.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1260513 0.2725202 midg,1,midg; midg,igrid,midg 0.3664569 0.1753127 1,midg,midg; igrid,midg,midg 0.4840244 -0.6427546 gauss-seidel spectral radius is 0.9993131 estimated iterations to convergence 301 setup time was (sec) 2.360000 now iterating at: 08:34:20 rms-change max change #iterations 10.67127 358.2944 at 10iterations 6.348724 128.9464 at 20iterations 3.768407 78.75130 at 30iterations 2.240712 53.35220 at 40iterations 1.326970 23.87214 at 50iterations 0.7835688 13.60183 at 60iterations 0.4630501 8.454729 at 70iterations 0.2740706 5.346653 at 80iterations 0.1614954 2.684975 at 90iterations 9.5294125E-02 1.627071 at 100iterations 5.6233507E-02 0.9914713 at 110iterations 3.3274166E-02 0.5508232 at 120iterations 1.9851407E-02 0.3378725 at 130iterations 1.1927405E-02 0.2168465 at 140iterations 7.3086568E-03 0.1410513 at 150iterations 4.6034120E-03 8.9569092E-02 at 160iterations 3.0340741E-03 5.4456711E-02 at 170iterations 2.1231107E-03 3.7662506E-02 at 180iterations finished qdiffx linear iterations at : 08:34:30 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 2.1231107E-03 3.7662506E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 08:34:31 13.137u 0.227s 0:13.86 96.3% 0+0k 0+0io 0pf+0w