Sun Oct 9 20:00:18 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 Sun Oct 9 2011 at 20:00:18 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5309 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5471451 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): 3.171000 67.61200 ymin,ymax (A): -8.822000 52.95100 zmin,zma (A): -2.171000 62.89400 x,y,z range (A): 64.44100 61.77300 65.06500 scale (grids/A): 0.5471451 object centre (A): 35.39150 22.06450 30.36150 number of atom coordinates read : 5309 total number of charged atoms : 5167 net assigned charge : 2.530052 assigned positive charge : 817.2514 centred at (gu) : 88.09914 89.26643 89.34213 assigned negative charge : -814.7275 centred at (gu) : 88.00045 89.28313 89.31258 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10118 nv = 96 ne = 84 npr = 109067 no. pairs analyzed = 109067 no. exposed pairs = 5955 no. arc points = 40823 no. surface atoms = 2033 nbur = 3276 mkacc time = 0.1900000 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 = 1.568000 m= 403 mr = 5819 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4164 ## 483 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 13526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1754171E-10 4.7968968E-10 midg,1,midg; midg,igrid,midg 4.8291249E-10 -1.5031131E-11 1,midg,midg; igrid,midg,midg -1.7440378E-09 8.9078911E-10 gauss-seidel spectral radius is 0.9829397 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 20:00:19 rms-change max change #iterations 0.1058042 12.81028 at 10iterations 1.0906894E-02 1.495399 at 20iterations 3.7689840E-03 0.5526505 at 30iterations 1.7056611E-03 0.2435112 at 40iterations 7.8442832E-04 0.1077805 at 50iterations finished qdiffx linear iterations at : 20:00:22 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 7.8442832E-04 0.1077805 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 20:00:22 3.613u 0.167s 0:04.10 91.9% 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 20:00:22 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5309 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 1.641435 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): 3.171000 67.61200 ymin,ymax (A): -8.822000 52.95100 zmin,zma (A): -2.171000 62.89400 x,y,z range (A): 64.44100 61.77300 65.06500 scale (grids/A): 1.641435 object centre (A): 35.39150 22.06450 30.36150 number of atom coordinates read : 5309 total number of charged atoms : 5167 net assigned charge : 2.530052 assigned positive charge : 817.2514 centred at (gu) : 84.29600 87.79790 88.02473 assigned negative charge : -814.7275 centred at (gu) : 84.00138 87.84946 87.93777 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 114805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 37325 mr = 83850 m= 4139 mr = 26728 m= 132 mr = 2086 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 681 time to turn everything in is 0.5600000 number of dielectric boundary points 43727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 440 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 39601 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) : 0.5471451 object centre at (A) : 35.39150 22.06450 30.36150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0493608E-02 -6.0515329E-03 midg,1,midg; midg,igrid,midg 1.8664453E-02 9.8104924E-03 1,midg,midg; igrid,midg,midg -1.7819958E-02 3.8595805E-03 gauss-seidel spectral radius is 0.9984063 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 20:00:23 rms-change max change #iterations 4.803481 181.8409 at 10iterations 2.121307 61.30289 at 20iterations 0.9355976 24.63797 at 30iterations 0.4144127 12.11924 at 40iterations 0.1847846 5.465607 at 50iterations 8.2214095E-02 2.144485 at 60iterations 3.7416458E-02 1.015030 at 70iterations 1.7753178E-02 0.5070572 at 80iterations 9.1597093E-03 0.2896194 at 90iterations 5.3857150E-03 0.1809464 at 100iterations 3.5531309E-03 0.1119537 at 110iterations 2.5129514E-03 7.5031281E-02 at 120iterations finished qdiffx linear iterations at : 20:00:31 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 2.5129514E-03 7.5031281E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 20:00:31 8.210u 0.202s 0:08.73 96.3% 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 20:00:31 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5309 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.462153 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): 3.171000 67.61200 ymin,ymax (A): -8.822000 52.95100 zmin,zma (A): -2.171000 62.89400 x,y,z range (A): 64.44100 61.77300 65.06500 scale (grids/A): 2.462153 object centre (A): 35.39150 22.06450 30.36150 number of atom coordinates read : 5309 total number of charged atoms : 5167 net assigned charge : 2.530052 assigned positive charge : 817.2514 centred at (gu) : 81.44366 86.69655 87.03675 assigned negative charge : -814.7275 centred at (gu) : 81.00211 86.77424 86.90652 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 267277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 129988 mr = 204148 m= 38376 mr = 105990 m= 6691 mr = 29372 m= 587 mr = 4423 m= 21 mr = 323 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 2176 time to turn everything in is 1.340000 number of dielectric boundary points 98684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 41289 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) : 1.641435 object centre at (A) : 35.39150 22.06450 30.36150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3436711 -0.1996423 midg,1,midg; midg,igrid,midg 0.1864717 3.5822038E-02 1,midg,midg; igrid,midg,midg -0.4231538 9.0025187E-02 gauss-seidel spectral radius is 0.9992452 estimated iterations to convergence 287 setup time was (sec) 1.580000 now iterating at: 20:00:33 rms-change max change #iterations 12.19881 321.4612 at 10iterations 7.160358 142.3438 at 20iterations 4.169526 79.76142 at 30iterations 2.420588 42.96230 at 40iterations 1.401090 24.64873 at 50iterations 0.8091009 14.43176 at 60iterations 0.4666039 8.982794 at 70iterations 0.2686533 4.783651 at 80iterations 0.1546310 2.342081 at 90iterations 8.9276262E-02 1.389145 at 100iterations 5.1652204E-02 0.8354578 at 110iterations 3.0184506E-02 0.5268977 at 120iterations 1.7951919E-02 0.3425484 at 130iterations 1.0950625E-02 0.2072296 at 140iterations 7.0400219E-03 0.1370533 at 150iterations 4.8147407E-03 9.8136902E-02 at 160iterations 3.5213865E-03 6.6314697E-02 at 170iterations 2.7096714E-03 5.1452637E-02 at 180iterations finished qdiffx linear iterations at : 20:00:45 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 2.7096714E-03 5.1452637E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 20:00:45 13.299u 0.210s 0:13.78 97.9% 0+0k 0+0io 0pf+0w