Tue Oct 11 07:15:16 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+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 Tue Oct 11 2011 at 07:15:16 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 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: 0.5917356 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): 0.6920000 48.95800 ymin,ymax (A): -8.689000 49.23000 zmin,zma (A): 0.9160000 61.07800 x,y,z range (A): 48.26600 57.91900 60.16200 scale (grids/A): 0.5917356 object centre (A): 24.82500 20.27050 30.99700 number of atom coordinates read : 3242 total number of charged atoms : 3090 net assigned charge : -0.5859914 assigned positive charge : 488.6298 centred at (gu) : 89.66268 89.62129 90.88638 assigned negative charge : -489.2169 centred at (gu) : 89.57133 89.53358 90.81326 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7483 nv = 96 ne = 84 npr = 66370 no. pairs analyzed = 66370 no. exposed pairs = 3870 no. arc points = 26145 no. surface atoms = 1322 nbur = 1920 mkacc time = 0.2200000 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 = 1.456000 m= 382 mr = 4320 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4600000 number of dielectric boundary points 3512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2643 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 9480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2812816E-09 2.9390033E-09 midg,1,midg; midg,igrid,midg -3.6389884E-09 2.6459159E-09 1,midg,midg; igrid,midg,midg -3.7465600E-09 2.7884404E-09 gauss-seidel spectral radius is 0.9852724 estimated iterations to convergence 68 setup time was (sec) 0.8700000 now iterating at: 07:15:17 rms-change max change #iterations 0.1163429 18.25533 at 10iterations 1.0113336E-02 1.579877 at 20iterations 1.2360847E-03 0.1961040 at 30iterations 3.5705906E-04 5.5985928E-02 at 40iterations 1.3240555E-04 2.0819187E-02 at 50iterations finished qdiffx linear iterations at : 07:15:21 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 1.3240555E-04 2.0819187E-02 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 07:15:22 4.628u 0.406s 0:05.63 89.1% 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 07:15:22 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 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: 1.775207 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): 0.6920000 48.95800 ymin,ymax (A): -8.689000 49.23000 zmin,zma (A): 0.9160000 61.07800 x,y,z range (A): 48.26600 57.91900 60.16200 scale (grids/A): 1.775207 object centre (A): 24.82500 20.27050 30.99700 number of atom coordinates read : 3242 total number of charged atoms : 3090 net assigned charge : -0.5859914 assigned positive charge : 488.6298 centred at (gu) : 88.98726 88.86276 92.65823 assigned negative charge : -489.2169 centred at (gu) : 88.71366 88.60080 92.43914 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 30271 mr = 59197 m= 4103 mr = 22915 m= 130 mr = 2518 m= 0 mr = 43 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 796 time to turn everything in is 0.8300000 number of dielectric boundary points 32548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 24060 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) : 0.5917356 object centre at (A) : 24.82500 20.27050 30.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3639509E-02 5.4389457E-03 midg,1,midg; midg,igrid,midg -1.5278614E-02 6.3003539E-03 1,midg,midg; igrid,midg,midg -1.0354778E-02 2.5810904E-03 gauss-seidel spectral radius is 0.9984982 estimated iterations to convergence 205 setup time was (sec) 1.170000 now iterating at: 07:15:23 rms-change max change #iterations 4.249278 162.6202 at 10iterations 1.916882 66.03532 at 20iterations 0.8683014 25.28243 at 30iterations 0.3937108 12.66781 at 40iterations 0.1783556 5.736084 at 50iterations 8.0966257E-02 2.622101 at 60iterations 3.6774430E-02 1.127621 at 70iterations 1.6753215E-02 0.5400925 at 80iterations 7.7002347E-03 0.2253070 at 90iterations 3.6303748E-03 0.1194205 at 100iterations 1.7886136E-03 6.1973572E-02 at 110iterations 9.4335584E-04 3.4918308E-02 at 120iterations finished qdiffx linear iterations at : 07:15:32 total time elapsed so far: 10.27000 # loops : 120 mean,max change (kT/e) : 9.4335584E-04 3.4918308E-02 energy calculations done at 10.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.49000 DelPhi exited at 07:15:33 10.495u 0.458s 0:11.49 95.2% 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 Tue Oct 11 2011 at 07:15:33 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 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: 2.662810 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): 0.6920000 48.95800 ymin,ymax (A): -8.689000 49.23000 zmin,zma (A): 0.9160000 61.07800 x,y,z range (A): 48.26600 57.91900 60.16200 scale (grids/A): 2.662810 object centre (A): 24.82500 20.27050 30.99700 number of atom coordinates read : 3242 total number of charged atoms : 3090 net assigned charge : -0.5859914 assigned positive charge : 488.6298 centred at (gu) : 88.48072 88.29410 93.98714 assigned negative charge : -489.2169 centred at (gu) : 88.07044 87.90105 93.65859 start vw surface at 0.1800000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 191494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 99727 mr = 143187 m= 34302 mr = 82913 m= 6935 mr = 28023 m= 702 mr = 5205 m= 17 mr = 428 m= 0 mr = 0 time to grow re-entrant surface = 1.330000 no. cavity mid-points inaccessible to solvent = 2693 time to turn everything in is 2.170000 number of dielectric boundary points 73421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 24711 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) : 1.775207 object centre at (A) : 24.82500 20.27050 30.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3336554 -6.4926215E-02 midg,1,midg; midg,igrid,midg -0.3095140 0.1055805 1,midg,midg; igrid,midg,midg -0.1218930 -1.0191076E-03 gauss-seidel spectral radius is 0.9992304 estimated iterations to convergence 285 setup time was (sec) 2.530000 now iterating at: 07:15:36 rms-change max change #iterations 10.29493 333.3987 at 10iterations 5.984928 145.9592 at 20iterations 3.453711 74.21374 at 30iterations 1.979077 43.40790 at 40iterations 1.137201 22.92027 at 50iterations 0.6508124 12.30091 at 60iterations 0.3724404 6.517663 at 70iterations 0.2121109 3.959328 at 80iterations 0.1210788 2.390329 at 90iterations 6.8997994E-02 1.155876 at 100iterations 3.9364312E-02 0.6934566 at 110iterations 2.2463661E-02 0.4159579 at 120iterations 1.2855554E-02 0.2467728 at 130iterations 7.4051302E-03 0.1315346 at 140iterations 4.3078577E-03 7.8241348E-02 at 150iterations 2.5678424E-03 4.8183441E-02 at 160iterations 1.5879741E-03 3.1536102E-02 at 170iterations 1.0340243E-03 2.0266533E-02 at 180iterations finished qdiffx linear iterations at : 07:15:51 total time elapsed so far: 17.77000 # loops : 180 mean,max change (kT/e) : 1.0340243E-03 2.0266533E-02 energy calculations done at 17.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.00000 DelPhi exited at 07:15:52 18.000u 0.469s 0:18.84 97.9% 0+0k 0+0io 0pf+0w