Sat Oct 8 14:22:58 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 Sat Oct 8 2011 at 14:22:58 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 = 3035 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6014834 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): -27.07800 23.49300 ymin,ymax (A): -34.84000 24.34700 zmin,zma (A): -27.75500 24.67600 x,y,z range (A): 50.57100 59.18700 52.43100 scale (grids/A): 0.6014834 object centre (A): -1.792500 -5.246500 -1.539501 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 7.1674585E-06 assigned positive charge : 454.5136 centred at (gu) : 91.45614 92.13051 91.12157 assigned negative charge : -454.5143 centred at (gu) : 91.50361 92.04237 91.19127 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7072 nv = 96 ne = 84 npr = 64313 no. pairs analyzed = 64313 no. exposed pairs = 3457 no. arc points = 24048 no. surface atoms = 1173 nbur = 1862 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 4074 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3400000 number of dielectric boundary points 3295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2442 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9056 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3575804E-09 -4.0639194E-09 midg,1,midg; midg,igrid,midg -2.4392974E-09 6.3351755E-09 1,midg,midg; igrid,midg,midg 1.4881800E-09 -2.9932892E-09 gauss-seidel spectral radius is 0.9857204 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 14:22:59 rms-change max change #iterations 0.1212775 18.27331 at 10iterations 1.0374495E-02 1.542114 at 20iterations 9.7280991E-04 0.1401348 at 30iterations 1.0950949E-04 1.5939713E-02 at 40iterations 1.7897299E-05 2.4833679E-03 at 50iterations finished qdiffx linear iterations at : 14:23:01 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.7897299E-05 2.4833679E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:23:02 3.370u 0.198s 0:03.91 91.0% 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 8 2011 at 14:23:02 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 = 3035 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.804450 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): -27.07800 23.49300 ymin,ymax (A): -34.84000 24.34700 zmin,zma (A): -27.75500 24.67600 x,y,z range (A): 50.57100 59.18700 52.43100 scale (grids/A): 1.804450 object centre (A): -1.792500 -5.246500 -1.539501 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 7.1674585E-06 assigned positive charge : 454.5136 centred at (gu) : 94.36787 96.39108 93.36410 assigned negative charge : -454.5143 centred at (gu) : 94.51044 96.12663 93.57365 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24048 grid for indexing accessible points = 1.400000 m= 26520 mr = 56197 m= 3260 mr = 19524 m= 123 mr = 1853 m= 0 mr = 25 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 101 time to turn everything in is 0.5400000 number of dielectric boundary points 30581 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 22574 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) : 0.6014834 object centre at (A) : -1.792500 -5.246500 -1.539501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3133931E-02 7.6762545E-03 midg,1,midg; midg,igrid,midg -1.3355534E-02 3.2086167E-02 1,midg,midg; igrid,midg,midg 4.0250011E-03 -1.0920579E-02 gauss-seidel spectral radius is 0.9985136 estimated iterations to convergence 206 setup time was (sec) 0.8300000 now iterating at: 14:23:03 rms-change max change #iterations 4.171795 162.9623 at 10iterations 1.891712 63.35767 at 20iterations 0.8583588 25.78386 at 30iterations 0.3909633 12.12326 at 40iterations 0.1769650 6.234003 at 50iterations 8.0384806E-02 2.637464 at 60iterations 3.6527395E-02 1.318649 at 70iterations 1.6645055E-02 0.5230179 at 80iterations 7.5739510E-03 0.2478180 at 90iterations 3.4427126E-03 0.1065598 at 100iterations 1.5700619E-03 5.1918983E-02 at 110iterations 7.1859278E-04 2.3185730E-02 at 120iterations finished qdiffx linear iterations at : 14:23:10 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 7.1859278E-04 2.3185730E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 14:23:11 7.952u 0.259s 0:08.56 95.7% 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 8 2011 at 14:23:11 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 = 3035 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.706676 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): -27.07800 23.49300 ymin,ymax (A): -34.84000 24.34700 zmin,zma (A): -27.75500 24.67600 x,y,z range (A): 50.57100 59.18700 52.43100 scale (grids/A): 2.706676 object centre (A): -1.792500 -5.246500 -1.539501 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 7.1674585E-06 assigned positive charge : 454.5136 centred at (gu) : 96.55189 99.58651 95.04616 assigned negative charge : -454.5143 centred at (gu) : 96.76566 99.18996 95.36037 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 181676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24048 grid for indexing accessible points = 1.400000 m= 89676 mr = 136363 m= 28645 mr = 73881 m= 5492 mr = 22650 m= 538 mr = 3909 m= 7 mr = 292 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 307 time to turn everything in is 1.370000 number of dielectric boundary points 68939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 23099 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) : 1.804450 object centre at (A) : -1.792500 -5.246500 -1.539501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1443528 0.2144897 midg,1,midg; midg,igrid,midg -9.3918070E-02 0.4485128 1,midg,midg; igrid,midg,midg 7.1096718E-02 -6.9153555E-02 gauss-seidel spectral radius is 0.9992276 estimated iterations to convergence 284 setup time was (sec) 1.690000 now iterating at: 14:23:12 rms-change max change #iterations 9.966254 330.7753 at 10iterations 5.752774 125.8620 at 20iterations 3.292698 67.70725 at 30iterations 1.883299 33.83860 at 40iterations 1.075032 21.05635 at 50iterations 0.6139128 13.31813 at 60iterations 0.3497799 7.082853 at 70iterations 0.1991567 3.486853 at 80iterations 0.1132759 1.992886 at 90iterations 6.4359576E-02 1.175938 at 100iterations 3.6601428E-02 0.6620178 at 110iterations 2.0756187E-02 0.4145737 at 120iterations 1.1845998E-02 0.2233543 at 130iterations 6.7369742E-03 0.1182529 at 140iterations 3.8256836E-03 6.7939758E-02 at 150iterations 2.1843787E-03 3.8874626E-02 at 160iterations 1.2420296E-03 2.2285461E-02 at 170iterations 7.1183254E-04 1.2413025E-02 at 180iterations finished qdiffx linear iterations at : 14:23:24 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 7.1183254E-04 1.2413025E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 14:23:24 13.155u 0.249s 0:13.69 97.8% 0+0k 0+0io 0pf+0w