Sun Oct 9 07:47:36 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 Sun Oct 9 2011 at 07:47:36 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7062091 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): -8.046000 33.63400 ymin,ymax (A): 1.940000 42.43200 zmin,zma (A): 9.408000 59.81800 x,y,z range (A): 41.68000 40.49200 50.41000 scale (grids/A): 0.7062091 object centre (A): 12.79400 22.18600 34.61300 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.4242 centred at (gu) : 91.57487 89.64834 89.66208 assigned negative charge : -262.9241 centred at (gu) : 91.33879 89.83324 89.88976 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5671 nv = 96 ne = 84 npr = 36418 no. pairs analyzed = 36418 no. exposed pairs = 2114 no. arc points = 14817 no. surface atoms = 709 nbur = 988 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 337 mr = 3141 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.1500000 number of dielectric boundary points 2807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1282 ## 88 charges are in solution ## iepsmp to db, and charging done at 0.2100000 number of grid points assigned charge 6269 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9361227E-09 -1.7824085E-07 midg,1,midg; midg,igrid,midg -2.3761293E-08 -1.6094921E-07 1,midg,midg; igrid,midg,midg -1.4315475E-07 -1.2867599E-09 gauss-seidel spectral radius is 0.9895144 estimated iterations to convergence 80 setup time was (sec) 0.3300000 now iterating at: 07:47:37 rms-change max change #iterations 0.1902605 29.09505 at 10iterations 2.2870660E-02 3.377792 at 20iterations 2.8014740E-03 0.4248810 at 30iterations 3.4239609E-04 4.9999237E-02 at 40iterations 4.1683626E-05 5.9563518E-03 at 50iterations finished qdiffx linear iterations at : 07:47:40 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 4.1683626E-05 5.9563518E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:47:40 3.321u 0.176s 0:03.76 92.8% 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 Sun Oct 9 2011 at 07:47:40 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.118627 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): -8.046000 33.63400 ymin,ymax (A): 1.940000 42.43200 zmin,zma (A): 9.408000 59.81800 x,y,z range (A): 41.68000 40.49200 50.41000 scale (grids/A): 2.118627 object centre (A): 12.79400 22.18600 34.61300 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.4242 centred at (gu) : 94.72479 88.94512 88.98662 assigned negative charge : -262.9241 centred at (gu) : 94.01652 89.49979 89.66924 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14817 grid for indexing accessible points = 1.400000 m= 23041 mr = 40763 m= 4443 mr = 17674 m= 350 mr = 3052 m= 9 mr = 130 m= 0 mr = 1 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1717 time to turn everything in is 0.3100000 number of dielectric boundary points 25813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12405 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) : 0.7062091 object centre at (A) : 12.79400 22.18600 34.61300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5352395E-02 -8.9004673E-02 midg,1,midg; midg,igrid,midg -9.3697971E-03 -5.2948751E-02 1,midg,midg; igrid,midg,midg -7.3726617E-02 -5.3549982E-03 gauss-seidel spectral radius is 0.9987906 estimated iterations to convergence 228 setup time was (sec) 0.5100000 now iterating at: 07:47:41 rms-change max change #iterations 4.223258 235.1514 at 10iterations 2.052530 74.88296 at 20iterations 1.005340 34.38711 at 30iterations 0.4925937 15.89145 at 40iterations 0.2409787 8.739177 at 50iterations 0.1177223 3.929247 at 60iterations 5.7726212E-02 1.762874 at 70iterations 2.8171806E-02 0.9539766 at 80iterations 1.3817455E-02 0.4483585 at 90iterations 6.7591472E-03 0.2406387 at 100iterations 3.3126343E-03 0.1216884 at 110iterations 1.6266848E-03 5.3268433E-02 at 120iterations finished qdiffx linear iterations at : 07:47:48 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.6266848E-03 5.3268433E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 07:47:48 7.610u 0.211s 0:08.10 96.5% 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 Sun Oct 9 2011 at 07:47:48 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.177941 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): -8.046000 33.63400 ymin,ymax (A): 1.940000 42.43200 zmin,zma (A): 9.408000 59.81800 x,y,z range (A): 41.68000 40.49200 50.41000 scale (grids/A): 3.177941 object centre (A): 12.79400 22.18600 34.61300 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.4242 centred at (gu) : 97.08728 88.41769 88.48001 assigned negative charge : -262.9241 centred at (gu) : 96.02467 89.24963 89.50394 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 137020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14817 grid for indexing accessible points = 1.400000 m= 71827 mr = 98333 m= 29462 mr = 59564 m= 8462 mr = 24533 m= 1509 mr = 6683 m= 104 mr = 1064 m= 7 mr = 51 m= 0 mr = 3 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 5739 time to turn everything in is 0.9200000 number of dielectric boundary points 58160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 12480 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) : 2.118627 object centre at (A) : 12.79400 22.18600 34.61300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4138410E-02 -0.6879387 midg,1,midg; midg,igrid,midg -9.4273418E-02 -0.4039090 1,midg,midg; igrid,midg,midg -0.6378571 -2.5445653E-02 gauss-seidel spectral radius is 0.9992803 estimated iterations to convergence 294 setup time was (sec) 1.150000 now iterating at: 07:47:50 rms-change max change #iterations 9.402806 435.2483 at 10iterations 5.445107 129.0869 at 20iterations 3.145506 75.44806 at 30iterations 1.825689 35.28921 at 40iterations 1.058201 22.31401 at 50iterations 0.6126722 13.22228 at 60iterations 0.3540520 6.650330 at 70iterations 0.2049351 4.263493 at 80iterations 0.1188378 2.556131 at 90iterations 6.8497717E-02 1.371998 at 100iterations 3.9633255E-02 0.7378058 at 110iterations 2.2901211E-02 0.5254593 at 120iterations 1.3283520E-02 0.2614422 at 130iterations 7.6719616E-03 0.1443214 at 140iterations 4.4393167E-03 8.2406044E-02 at 150iterations 2.5639245E-03 4.6352386E-02 at 160iterations 1.4834345E-03 2.8511047E-02 at 170iterations 8.5848832E-04 1.5642166E-02 at 180iterations finished qdiffx linear iterations at : 07:48:01 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 8.5848832E-04 1.5642166E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 07:48:01 12.358u 0.207s 0:12.83 97.8% 0+0k 0+0io 0pf+0w