Wed Feb 15 08:58:38 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:58:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 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: 0.6010062 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 0.6010062 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 89.04030 89.55356 88.55474 assigned negative charge : -425.1732 centred at (gu) : 88.90827 89.71317 88.59105 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7780 nv = 96 ne = 84 npr = 63100 no. pairs analyzed = 63100 no. exposed pairs = 4637 no. arc points = 32606 no. surface atoms = 1557 nbur = 1551 mkacc time = 0.1700000 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 = 1.456000 m= 416 mr = 3477 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3104 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9182422E-09 -1.0163340E-10 midg,1,midg; midg,igrid,midg 8.6139700E-09 -4.8188387E-09 1,midg,midg; igrid,midg,midg -5.2385909E-09 5.3712039E-09 gauss-seidel spectral radius is 0.9857420 estimated iterations to convergence 69 setup time was (sec) 0.8800000 now iterating at: 08:58:39 rms-change max change #iterations 0.1103869 18.44469 at 10iterations 1.0613686E-02 1.514076 at 20iterations 2.5789880E-03 0.4376068 at 30iterations 1.1186873E-03 0.1968918 at 40iterations 5.0731521E-04 8.9569092E-02 at 50iterations finished qdiffx linear iterations at : 08:58:47 total time elapsed so far: 8.370000 # loops : 50 mean,max change (kT/e) : 5.0731521E-04 8.9569092E-02 energy calculations done at 8.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.540000 DelPhi exited at 08:58:47 8.547u 0.733s 0:09.75 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 Wed Feb 15 2012 at 08:58:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 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: 1.803018 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 1.803018 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 87.11962 88.65971 85.66330 assigned negative charge : -425.1732 centred at (gu) : 86.72475 89.13952 85.77279 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 83377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32606 grid for indexing accessible points = 1.400000 m= 26847 mr = 51799 m= 3925 mr = 16961 m= 188 mr = 1978 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 43565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 23217 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) : 0.6010062 object centre at (A) : 15.02300 16.60800 23.75700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0377936E-03 1.1109034E-02 midg,1,midg; midg,igrid,midg -8.0208183E-04 1.6759440E-03 1,midg,midg; igrid,midg,midg -1.3364813E-02 5.1257201E-02 gauss-seidel spectral radius is 0.9985718 estimated iterations to convergence 210 setup time was (sec) 1.060000 now iterating at: 08:58:49 rms-change max change #iterations 4.025448 185.5009 at 10iterations 1.831025 72.92381 at 20iterations 0.8394576 28.59912 at 30iterations 0.3852400 12.60678 at 40iterations 0.1769402 5.989660 at 50iterations 8.1427127E-02 2.714880 at 60iterations 3.7652135E-02 1.292690 at 70iterations 1.7783351E-02 0.5725555 at 80iterations 8.7868432E-03 0.2900543 at 90iterations 4.7096824E-03 0.1966400 at 100iterations 2.8512641E-03 0.1150742 at 110iterations 1.9517309E-03 6.9538116E-02 at 120iterations finished qdiffx linear iterations at : 08:58:59 total time elapsed so far: 10.84000 # loops : 120 mean,max change (kT/e) : 1.9517309E-03 6.9538116E-02 energy calculations done at 10.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.01000 DelPhi exited at 08:59:00 11.012u 0.573s 0:12.04 96.1% 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 Wed Feb 15 2012 at 08:59:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 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: 2.704528 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 2.704528 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 85.67937 87.98929 83.49477 assigned negative charge : -425.1732 centred at (gu) : 85.08704 88.70920 83.65896 start vw surface at 0.1300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 192894 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32606 grid for indexing accessible points = 1.400000 m= 87239 mr = 128149 m= 29715 mr = 64948 m= 6581 mr = 21214 m= 759 mr = 4278 m= 34 mr = 375 m= 0 mr = 1 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.790000 number of dielectric boundary points 98257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 23758 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) : 1.803018 object centre at (A) : 15.02300 16.60800 23.75700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8742470E-02 0.1178054 midg,1,midg; midg,igrid,midg -0.1175928 -2.4168801E-02 1,midg,midg; igrid,midg,midg -0.5512573 0.7019312 gauss-seidel spectral radius is 0.9992795 estimated iterations to convergence 294 setup time was (sec) 2.200000 now iterating at: 08:59:02 rms-change max change #iterations 10.06759 312.0682 at 10iterations 6.135569 162.4502 at 20iterations 3.695838 86.20184 at 30iterations 2.203134 58.83640 at 40iterations 1.308108 26.18186 at 50iterations 0.7725649 15.83472 at 60iterations 0.4547287 9.962430 at 70iterations 0.2666860 5.448776 at 80iterations 0.1561163 2.829018 at 90iterations 9.1361374E-02 1.724762 at 100iterations 5.3382978E-02 1.124256 at 110iterations 3.1241829E-02 0.6428680 at 120iterations 1.8327581E-02 0.3210793 at 130iterations 1.0823870E-02 0.2283335 at 140iterations 6.5126242E-03 0.1420174 at 150iterations 4.0457034E-03 7.8372955E-02 at 160iterations 2.6532824E-03 5.6301117E-02 at 170iterations 1.8674308E-03 3.9360046E-02 at 180iterations finished qdiffx linear iterations at : 08:59:19 total time elapsed so far: 19.19000 # loops : 180 mean,max change (kT/e) : 1.8674308E-03 3.9360046E-02 energy calculations done at 19.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.36000 DelPhi exited at 08:59:20 19.368u 0.475s 0:20.22 98.0% 0+0k 0+0io 0pf+0w