Sat Oct 15 11:28:46 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 Sat Oct 15 2011 at 11:28:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6237735 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): -31.79500 17.77000 ymin,ymax (A): -24.18100 23.42700 zmin,zma (A): -12.33700 44.73500 x,y,z range (A): 49.56500 47.60800 57.07200 scale (grids/A): 0.6237735 object centre (A): -7.012500 -0.3769999 16.19900 number of atom coordinates read : 2589 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.2441 centred at (gu) : 88.63396 89.14691 89.66691 assigned negative charge : -388.3385 centred at (gu) : 88.52583 89.19404 89.55456 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6554 nv = 96 ne = 84 npr = 54410 no. pairs analyzed = 54410 no. exposed pairs = 3000 no. arc points = 21221 no. surface atoms = 1006 nbur = 1583 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 323 mr = 3679 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.2000000 number of dielectric boundary points 3157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2133 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8175 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1487410E-09 1.1017320E-08 midg,1,midg; midg,igrid,midg 8.5734371E-09 1.4939110E-10 1,midg,midg; igrid,midg,midg -6.1267214E-09 8.5755643E-09 gauss-seidel spectral radius is 0.9866840 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 11:28:47 rms-change max change #iterations 0.1315469 18.72215 at 10iterations 1.2331225E-02 2.001244 at 20iterations 1.1650997E-03 0.1686497 at 30iterations 1.0906691E-04 1.4826775E-02 at 40iterations 1.0265093E-05 1.7108917E-03 at 50iterations finished qdiffx linear iterations at : 11:28:50 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 1.0265093E-05 1.7108917E-03 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 11:28:51 3.891u 0.258s 0:04.53 91.3% 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 Sat Oct 15 2011 at 11:28:51 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.871320 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): -31.79500 17.77000 ymin,ymax (A): -24.18100 23.42700 zmin,zma (A): -12.33700 44.73500 x,y,z range (A): 49.56500 47.60800 57.07200 scale (grids/A): 1.871320 object centre (A): -7.012500 -0.3769999 16.19900 number of atom coordinates read : 2589 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.2441 centred at (gu) : 85.90141 87.44016 89.00057 assigned negative charge : -388.3385 centred at (gu) : 85.57700 87.58193 88.66364 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 71623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21221 grid for indexing accessible points = 1.400000 m= 24547 mr = 50269 m= 3293 mr = 18241 m= 169 mr = 1947 m= 0 mr = 60 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3498 time to turn everything in is 0.3800000 number of dielectric boundary points 29115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 19239 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) : 0.6237735 object centre at (A) : -7.012500 -0.3769999 16.19900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3213407E-02 2.2082882E-02 midg,1,midg; midg,igrid,midg 1.4712220E-02 4.2556059E-03 1,midg,midg; igrid,midg,midg -4.9370793E-03 3.8010668E-02 gauss-seidel spectral radius is 0.9985819 estimated iterations to convergence 211 setup time was (sec) 0.6600000 now iterating at: 11:28:52 rms-change max change #iterations 4.120055 173.2157 at 10iterations 1.895803 68.19760 at 20iterations 0.8753718 28.73429 at 30iterations 0.4039077 13.37371 at 40iterations 0.1869800 6.094184 at 50iterations 8.6047493E-02 2.807909 at 60iterations 3.9810836E-02 1.296120 at 70iterations 1.8406827E-02 0.6463223 at 80iterations 8.4822206E-03 0.2591562 at 90iterations 3.9152210E-03 0.1240683 at 100iterations 1.8057948E-03 6.7364693E-02 at 110iterations 8.3635992E-04 2.6386261E-02 at 120iterations finished qdiffx linear iterations at : 11:28:59 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 8.3635992E-04 2.6386261E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 11:29:00 8.406u 0.257s 0:09.02 95.8% 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 Sat Oct 15 2011 at 11:29:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.806981 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): -31.79500 17.77000 ymin,ymax (A): -24.18100 23.42700 zmin,zma (A): -12.33700 44.73500 x,y,z range (A): 49.56500 47.60800 57.07200 scale (grids/A): 2.806981 object centre (A): -7.012500 -0.3769999 16.19900 number of atom coordinates read : 2589 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.2441 centred at (gu) : 83.85188 86.16020 88.50078 assigned negative charge : -388.3385 centred at (gu) : 83.36546 86.37292 87.99537 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 165835 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21221 grid for indexing accessible points = 1.400000 m= 81704 mr = 121756 m= 27095 mr = 67463 m= 5745 mr = 21541 m= 688 mr = 4210 m= 30 mr = 451 m= 0 mr = 11 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 12123 time to turn everything in is 0.9600000 number of dielectric boundary points 65665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 19600 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) : 1.871320 object centre at (A) : -7.012500 -0.3769999 16.19900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1565745 0.2494873 midg,1,midg; midg,igrid,midg 0.1737059 2.9375684E-02 1,midg,midg; igrid,midg,midg -3.9739031E-02 0.4955143 gauss-seidel spectral radius is 0.9992387 estimated iterations to convergence 286 setup time was (sec) 1.240000 now iterating at: 11:29:01 rms-change max change #iterations 9.619223 264.7430 at 10iterations 5.534814 138.9942 at 20iterations 3.171440 61.08948 at 30iterations 1.811925 38.07312 at 40iterations 1.038769 23.93283 at 50iterations 0.5922025 13.16147 at 60iterations 0.3376485 6.559244 at 70iterations 0.1926278 3.515952 at 80iterations 0.1099098 2.042221 at 90iterations 6.2638029E-02 1.246710 at 100iterations 3.5648193E-02 0.7620430 at 110iterations 2.0379525E-02 0.3665266 at 120iterations 1.1590540E-02 0.2340298 at 130iterations 6.6066980E-03 0.1265717 at 140iterations 3.7735773E-03 7.0960045E-02 at 150iterations 2.1466846E-03 3.8405895E-02 at 160iterations 1.2209940E-03 2.6187897E-02 at 170iterations 6.9637876E-04 1.3046265E-02 at 180iterations finished qdiffx linear iterations at : 11:29:14 total time elapsed so far: 13.61000 # loops : 180 mean,max change (kT/e) : 6.9637876E-04 1.3046265E-02 energy calculations done at 13.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 11:29:15 13.744u 0.302s 0:14.77 95.0% 0+0k 0+0io 0pf+0w