Mon Oct 10 13:55:54 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 Mon Oct 10 2011 at 13:55:55 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5006 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5595373 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): 3.191000 64.75000 ymin,ymax (A): -8.671000 52.58900 zmin,zma (A): -1.898000 61.72600 x,y,z range (A): 61.55900 61.26000 63.62400 scale (grids/A): 0.5595373 object centre (A): 33.97050 21.95900 29.91400 number of atom coordinates read : 5006 total number of charged atoms : 4890 net assigned charge : 1.621045 assigned positive charge : 775.8246 centred at (gu) : 88.39033 89.38644 89.11709 assigned negative charge : -774.2095 centred at (gu) : 88.22564 89.40639 89.11306 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 10180 nv = 96 ne = 84 npr = 100692 no. pairs analyzed = 100692 no. exposed pairs = 5977 no. arc points = 40574 no. surface atoms = 2019 nbur = 2987 mkacc time = 0.2700000 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 = 1.512000 m= 474 mr = 5716 m= 0 mr = 23 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 4915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4140 ## 447 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 13397 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8368941E-10 2.4430219E-10 midg,1,midg; midg,igrid,midg 6.9847889E-10 -1.2993603E-10 1,midg,midg; igrid,midg,midg -4.4085633E-09 2.2139548E-09 gauss-seidel spectral radius is 0.9836721 estimated iterations to convergence 64 setup time was (sec) 0.9000000 now iterating at: 13:55:58 rms-change max change #iterations 0.1140196 13.60174 at 10iterations 1.0323184E-02 1.377304 at 20iterations 3.0531653E-03 0.3563824 at 30iterations 1.5110743E-03 0.1715641 at 40iterations 7.6684990E-04 8.5422516E-02 at 50iterations finished qdiffx linear iterations at : 13:56:03 total time elapsed so far: 5.620000 # loops : 50 mean,max change (kT/e) : 7.6684990E-04 8.5422516E-02 energy calculations done at 5.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.770000 DelPhi exited at 13:56:03 5.775u 0.644s 0:08.62 74.3% 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 Mon Oct 10 2011 at 13:56:04 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5006 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.678612 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): 3.191000 64.75000 ymin,ymax (A): -8.671000 52.58900 zmin,zma (A): -1.898000 61.72600 x,y,z range (A): 61.55900 61.26000 63.62400 scale (grids/A): 1.678612 object centre (A): 33.97050 21.95900 29.91400 number of atom coordinates read : 5006 total number of charged atoms : 4890 net assigned charge : 1.621045 assigned positive charge : 775.8246 centred at (gu) : 85.16982 88.15800 87.34940 assigned negative charge : -774.2095 centred at (gu) : 84.67679 88.21897 87.33895 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 113047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40574 grid for indexing accessible points = 1.400000 m= 38639 mr = 81410 m= 4938 mr = 27274 m= 178 mr = 2622 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 45481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 37603 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) : 0.5595373 object centre at (A) : 33.97050 21.95900 29.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2013729E-02 -2.7886912E-02 midg,1,midg; midg,igrid,midg 1.8261677E-02 1.0399209E-02 1,midg,midg; igrid,midg,midg -2.4891831E-02 3.8836055E-02 gauss-seidel spectral radius is 0.9984701 estimated iterations to convergence 203 setup time was (sec) 1.310000 now iterating at: 13:56:08 rms-change max change #iterations 4.915938 187.4795 at 10iterations 2.200491 62.50401 at 20iterations 0.9889992 30.85478 at 30iterations 0.4439746 12.42213 at 40iterations 0.2002077 5.955346 at 50iterations 9.0318114E-02 2.449799 at 60iterations 4.1120149E-02 1.109753 at 70iterations 1.9131750E-02 0.5274937 at 80iterations 9.4451653E-03 0.2593765 at 90iterations 5.2411188E-03 0.1446304 at 100iterations 3.3713519E-03 9.2269897E-02 at 110iterations 2.4196005E-03 6.1103821E-02 at 120iterations finished qdiffx linear iterations at : 13:56:19 total time elapsed so far: 11.39000 # loops : 120 mean,max change (kT/e) : 2.4196005E-03 6.1103821E-02 energy calculations done at 11.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 13:56:19 11.563u 0.799s 0:14.97 82.4% 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 Mon Oct 10 2011 at 13:56:19 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5006 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.517918 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): 3.191000 64.75000 ymin,ymax (A): -8.671000 52.58900 zmin,zma (A): -1.898000 61.72600 x,y,z range (A): 61.55900 61.26000 63.62400 scale (grids/A): 2.517918 object centre (A): 33.97050 21.95900 29.91400 number of atom coordinates read : 5006 total number of charged atoms : 4890 net assigned charge : 1.621045 assigned positive charge : 775.8246 centred at (gu) : 82.75435 87.23652 86.02361 assigned negative charge : -774.2095 centred at (gu) : 82.01509 87.32838 86.00854 start vw surface at 0.1700000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 262898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40574 grid for indexing accessible points = 1.400000 m= 130238 mr = 198279 m= 41611 mr = 104975 m= 8085 mr = 31726 m= 759 mr = 5358 m= 17 mr = 355 m= 0 mr = 0 time to grow re-entrant surface = 1.480000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.340000 number of dielectric boundary points 102915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 39094 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) : 1.678612 object centre at (A) : 33.97050 21.95900 29.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3902424 -0.6324707 midg,1,midg; midg,igrid,midg 8.3015554E-02 -4.1293120E-03 1,midg,midg; igrid,midg,midg -0.3794090 0.4556494 gauss-seidel spectral radius is 0.9992655 estimated iterations to convergence 291 setup time was (sec) 2.700000 now iterating at: 13:56:23 rms-change max change #iterations 12.45707 323.8174 at 10iterations 7.399284 140.9526 at 20iterations 4.366408 89.65187 at 30iterations 2.570086 50.28905 at 40iterations 1.504974 27.11216 at 50iterations 0.8779210 18.09085 at 60iterations 0.5113541 9.255180 at 70iterations 0.2967454 4.786359 at 80iterations 0.1722608 3.087044 at 90iterations 9.9851191E-02 1.615219 at 100iterations 5.7875566E-02 0.9684143 at 110iterations 3.3668939E-02 0.5507360 at 120iterations 1.9652067E-02 0.3413734 at 130iterations 1.1547217E-02 0.1906548 at 140iterations 6.9596586E-03 0.1155679 at 150iterations 4.3514846E-03 7.7737808E-02 at 160iterations 2.8919065E-03 5.4756165E-02 at 170iterations 2.0692132E-03 3.9558411E-02 at 180iterations finished qdiffx linear iterations at : 13:56:43 total time elapsed so far: 20.97000 # loops : 180 mean,max change (kT/e) : 2.0692132E-03 3.9558411E-02 energy calculations done at 20.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.14000 DelPhi exited at 13:56:44 21.141u 0.731s 0:24.69 88.5% 0+0k 0+0io 0pf+0w