Mon Oct 10 09:14:15 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 Mon Oct 10 2011 at 09:14:15 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6469551 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): -6.185000 34.43400 ymin,ymax (A): -3.521000 47.90800 zmin,zma (A): -24.11200 30.91500 x,y,z range (A): 40.61900 51.42900 55.02700 scale (grids/A): 0.6469551 object centre (A): 14.12450 22.19350 3.401501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.6259 centred at (gu) : 90.92347 92.57336 90.15621 assigned negative charge : -289.6262 centred at (gu) : 91.02489 92.69653 90.11656 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5560 nv = 96 ne = 84 npr = 40561 no. pairs analyzed = 40561 no. exposed pairs = 2437 no. arc points = 17025 no. surface atoms = 826 nbur = 1138 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 3130 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.2700000 number of dielectric boundary points 2680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1659 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5808337E-09 1.0203055E-08 midg,1,midg; midg,igrid,midg 1.0742329E-08 -1.2999240E-08 1,midg,midg; igrid,midg,midg 1.3333765E-08 -6.0609833E-09 gauss-seidel spectral radius is 0.9875614 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 09:14:16 rms-change max change #iterations 0.1367038 21.66732 at 10iterations 1.3796128E-02 2.210329 at 20iterations 1.3845897E-03 0.2258084 at 30iterations 1.3960611E-04 2.3315430E-02 at 40iterations 1.4040034E-05 2.1195412E-03 at 50iterations finished qdiffx linear iterations at : 09:14:18 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.4040034E-05 2.1195412E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:14:19 3.369u 0.157s 0:03.93 89.3% 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 09:14:19 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.940865 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): -6.185000 34.43400 ymin,ymax (A): -3.521000 47.90800 zmin,zma (A): -24.11200 30.91500 x,y,z range (A): 40.61900 51.42900 55.02700 scale (grids/A): 1.940865 object centre (A): 14.12450 22.19350 3.401501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.6259 centred at (gu) : 92.77025 97.71996 90.46861 assigned negative charge : -289.6262 centred at (gu) : 93.07484 98.08958 90.34979 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59949 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17025 grid for indexing accessible points = 1.400000 m= 21838 mr = 41659 m= 3375 mr = 16612 m= 168 mr = 2252 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1432 time to turn everything in is 0.4700000 number of dielectric boundary points 24751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14457 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) : 0.6469551 object centre at (A) : 14.12450 22.19350 3.401501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7490720E-02 1.5960623E-02 midg,1,midg; midg,igrid,midg 3.4709260E-02 -6.8087028E-03 1,midg,midg; igrid,midg,midg 9.7987875E-03 -5.9715295E-03 gauss-seidel spectral radius is 0.9986037 estimated iterations to convergence 212 setup time was (sec) 0.7600000 now iterating at: 09:14:20 rms-change max change #iterations 3.761160 168.5685 at 10iterations 1.751493 68.27985 at 20iterations 0.8152508 28.85465 at 30iterations 0.3778546 12.65240 at 40iterations 0.1757762 6.358910 at 50iterations 8.1240661E-02 2.886929 at 60iterations 3.7673097E-02 1.369776 at 70iterations 1.7570017E-02 0.6540036 at 80iterations 8.1229359E-03 0.2885723 at 90iterations 3.7858759E-03 0.1313324 at 100iterations 1.7449227E-03 5.8731079E-02 at 110iterations 8.1344158E-04 3.2848835E-02 at 120iterations finished qdiffx linear iterations at : 09:14:26 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 8.1344158E-04 3.2848835E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 09:14:27 7.430u 0.208s 0:08.04 94.9% 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 Mon Oct 10 2011 at 09:14:27 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.911298 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): -6.185000 34.43400 ymin,ymax (A): -3.521000 47.90800 zmin,zma (A): -24.11200 30.91500 x,y,z range (A): 40.61900 51.42900 55.02700 scale (grids/A): 2.911298 object centre (A): 14.12450 22.19350 3.401501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.6259 centred at (gu) : 94.15541 101.5798 90.70301 assigned negative charge : -289.6262 centred at (gu) : 94.61241 102.1343 90.52473 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17025 grid for indexing accessible points = 1.400000 m= 70393 mr = 100489 m= 25733 mr = 58585 m= 6058 mr = 21409 m= 801 mr = 4709 m= 33 mr = 554 m= 0 mr = 13 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 4555 time to turn everything in is 1.180000 number of dielectric boundary points 55795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 14656 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) : 1.940865 object centre at (A) : 14.12450 22.19350 3.401501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.033896 3.2288332E-02 midg,1,midg; midg,igrid,midg 0.3483888 -0.1018876 1,midg,midg; igrid,midg,midg 6.9542453E-02 -3.8408399E-02 gauss-seidel spectral radius is 0.9992361 estimated iterations to convergence 286 setup time was (sec) 1.480000 now iterating at: 09:14:29 rms-change max change #iterations 8.730314 384.0173 at 10iterations 5.001631 117.1640 at 20iterations 2.839245 64.80978 at 30iterations 1.614592 36.41214 at 40iterations 0.9185116 20.82681 at 50iterations 0.5211306 12.08602 at 60iterations 0.2964020 5.933987 at 70iterations 0.1682430 3.618085 at 80iterations 9.5476240E-02 1.767567 at 90iterations 5.4249492E-02 1.013494 at 100iterations 3.0783826E-02 0.5928307 at 110iterations 1.7471928E-02 0.3285322 at 120iterations 9.9287257E-03 0.2011299 at 130iterations 5.6350995E-03 0.1183214 at 140iterations 3.2080852E-03 6.3888550E-02 at 150iterations 1.8211922E-03 3.8262367E-02 at 160iterations 1.0349224E-03 2.0256996E-02 at 170iterations 5.8794423E-04 1.2897491E-02 at 180iterations finished qdiffx linear iterations at : 09:14:39 total time elapsed so far: 11.51000 # loops : 180 mean,max change (kT/e) : 5.8794423E-04 1.2897491E-02 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 09:14:39 11.716u 0.222s 0:12.27 97.2% 0+0k 0+0io 0pf+0w