Sun Oct 9 16:08:24 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 16:08:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3120 !!! WARNING: GLM 240 has a net charge of -0.0940 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: 0.6324392 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): -15.20700 36.89800 ymin,ymax (A): 55.67600 107.8860 zmin,zma (A): -3.868000 52.42200 x,y,z range (A): 52.10500 52.21000 56.29000 scale (grids/A): 0.6324392 object centre (A): 10.84550 81.78101 24.27700 number of atom coordinates read : 3120 total number of charged atoms : 2971 net assigned charge : -4.593983 assigned positive charge : 462.7809 centred at (gu) : 90.09592 88.53714 91.19276 assigned negative charge : -467.3763 centred at (gu) : 90.14329 88.39919 91.26830 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8227 nv = 96 ne = 84 npr = 64836 no. pairs analyzed = 64836 no. exposed pairs = 3889 no. arc points = 26731 no. surface atoms = 1324 nbur = 1796 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 500 mr = 4478 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2623 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10084 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6771927E-09 -1.7636784E-08 midg,1,midg; midg,igrid,midg -2.8767881E-08 7.5411677E-09 1,midg,midg; igrid,midg,midg 3.8088310E-10 -1.0578088E-08 gauss-seidel spectral radius is 0.9870933 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 16:08:25 rms-change max change #iterations 0.1552895 23.09516 at 10iterations 1.4836609E-02 2.131413 at 20iterations 1.4364813E-03 0.1960859 at 30iterations 1.3854601E-04 1.7630577E-02 at 40iterations 1.3888740E-05 1.9035339E-03 at 50iterations finished qdiffx linear iterations at : 16:08:28 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.3888740E-05 1.9035339E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 16:08:28 3.417u 0.152s 0:03.84 92.7% 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 Sun Oct 9 2011 at 16:08:28 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3120 !!! WARNING: GLM 240 has a net charge of -0.0940 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: 1.897318 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): -15.20700 36.89800 ymin,ymax (A): 55.67600 107.8860 zmin,zma (A): -3.868000 52.42200 x,y,z range (A): 52.10500 52.21000 56.29000 scale (grids/A): 1.897318 object centre (A): 10.84550 81.78101 24.27700 number of atom coordinates read : 3120 total number of charged atoms : 2971 net assigned charge : -4.593983 assigned positive charge : 462.7809 centred at (gu) : 90.28692 85.61062 93.57744 assigned negative charge : -467.3763 centred at (gu) : 90.42986 85.19740 93.80467 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 89086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26731 grid for indexing accessible points = 1.400000 m= 32143 mr = 62005 m= 5430 mr = 23097 m= 313 mr = 3318 m= 6 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 193 time to turn everything in is 0.6800000 number of dielectric boundary points 38461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23402 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) : 0.6324392 object centre at (A) : 10.84550 81.78101 24.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3286000E-02 1.0959847E-02 midg,1,midg; midg,igrid,midg -3.5496291E-02 -9.6120806E-03 1,midg,midg; igrid,midg,midg -3.5398744E-02 -3.4093097E-02 gauss-seidel spectral radius is 0.9986684 estimated iterations to convergence 217 setup time was (sec) 0.9700000 now iterating at: 16:08:29 rms-change max change #iterations 4.649807 206.2347 at 10iterations 2.195103 80.67676 at 20iterations 1.036400 31.63004 at 30iterations 0.4886310 13.64782 at 40iterations 0.2318321 7.289135 at 50iterations 0.1095990 3.184517 at 60iterations 5.1820453E-02 1.544743 at 70iterations 2.4484238E-02 0.6959534 at 80iterations 1.1557227E-02 0.3378067 at 90iterations 5.4659601E-03 0.1606560 at 100iterations 2.5868448E-03 8.5927010E-02 at 110iterations 1.2265649E-03 3.6322713E-02 at 120iterations finished qdiffx linear iterations at : 16:08:36 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.2265649E-03 3.6322713E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 16:08:37 7.695u 0.158s 0:08.25 95.0% 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 Sun Oct 9 2011 at 16:08:37 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3120 !!! WARNING: GLM 240 has a net charge of -0.0940 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: 2.845976 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): -15.20700 36.89800 ymin,ymax (A): 55.67600 107.8860 zmin,zma (A): -3.868000 52.42200 x,y,z range (A): 52.10500 52.21000 56.29000 scale (grids/A): 2.845976 object centre (A): 10.84550 81.78101 24.27700 number of atom coordinates read : 3120 total number of charged atoms : 2971 net assigned charge : -4.593983 assigned positive charge : 462.7809 centred at (gu) : 90.43000 83.41580 95.36599 assigned negative charge : -467.3763 centred at (gu) : 90.64474 82.79610 95.70686 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 206507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26731 grid for indexing accessible points = 1.400000 m= 103262 mr = 151149 m= 38597 mr = 83285 m= 9935 mr = 30319 m= 1331 mr = 7332 m= 67 mr = 836 m= 0 mr = 32 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 1.720000 number of dielectric boundary points 86746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 23765 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) : 1.897318 object centre at (A) : 10.84550 81.78101 24.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4694520 0.2756043 midg,1,midg; midg,igrid,midg -0.3763041 -0.2297747 1,midg,midg; igrid,midg,midg -0.5098113 -0.3473894 gauss-seidel spectral radius is 0.9992798 estimated iterations to convergence 294 setup time was (sec) 2.020000 now iterating at: 16:08:39 rms-change max change #iterations 10.90271 327.0645 at 10iterations 6.424027 146.5950 at 20iterations 3.760110 70.39064 at 30iterations 2.196253 45.68087 at 40iterations 1.283484 23.10865 at 50iterations 0.7474567 13.25194 at 60iterations 0.4350551 7.794044 at 70iterations 0.2532045 4.790183 at 80iterations 0.1472008 2.453327 at 90iterations 8.5530020E-02 1.571291 at 100iterations 4.9666744E-02 1.023760 at 110iterations 2.8812973E-02 0.5282097 at 120iterations 1.6684726E-02 0.2828140 at 130iterations 9.6762907E-03 0.1649175 at 140iterations 5.6305053E-03 9.9457026E-02 at 150iterations 3.2545186E-03 5.5008650E-02 at 160iterations 1.8893931E-03 3.1757355E-02 at 170iterations 1.0970315E-03 1.9501686E-02 at 180iterations finished qdiffx linear iterations at : 16:08:49 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 1.0970315E-03 1.9501686E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 16:08:50 12.777u 0.183s 0:13.24 97.8% 0+0k 0+0io 0pf+0w