Sat Oct 8 23:25:35 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 8 2011 at 23:25:35 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2144 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: 0.6476024 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): -1.589000 53.38300 ymin,ymax (A): -15.83500 27.52100 zmin,zma (A): 32.70800 84.16400 x,y,z range (A): 54.97200 43.35600 51.45600 scale (grids/A): 0.6476024 object centre (A): 25.89700 5.843000 58.43600 number of atom coordinates read : 2144 total number of charged atoms : 2010 net assigned charge : 10.50002 assigned positive charge : 314.0828 centred at (gu) : 90.53056 88.74154 89.18581 assigned negative charge : -303.5833 centred at (gu) : 90.49293 88.82398 89.23073 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6104 nv = 96 ne = 84 npr = 43153 no. pairs analyzed = 43153 no. exposed pairs = 2811 no. arc points = 20069 no. surface atoms = 946 nbur = 1198 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 332 mr = 3146 m= 0 mr = 34 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2500000 number of dielectric boundary points 3256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1960 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7185 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8092206E-08 1.1639000E-08 midg,1,midg; midg,igrid,midg 3.6266471E-08 7.4168423E-09 1,midg,midg; igrid,midg,midg 1.3045449E-08 2.5574334E-08 gauss-seidel spectral radius is 0.9876088 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 23:25:36 rms-change max change #iterations 0.1367188 21.03011 at 10iterations 1.3584535E-02 1.983946 at 20iterations 1.4015762E-03 0.2117531 at 30iterations 1.4768673E-04 2.0782471E-02 at 40iterations 1.8492845E-05 2.4967194E-03 at 50iterations finished qdiffx linear iterations at : 23:25:39 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.8492845E-05 2.4967194E-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) 3.400000 DelPhi exited at 23:25:39 3.406u 0.246s 0:03.94 92.3% 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 8 2011 at 23:25:39 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2144 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: 1.942807 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): -1.589000 53.38300 ymin,ymax (A): -15.83500 27.52100 zmin,zma (A): 32.70800 84.16400 x,y,z range (A): 54.97200 43.35600 51.45600 scale (grids/A): 1.942807 object centre (A): 25.89700 5.843000 58.43600 number of atom coordinates read : 2144 total number of charged atoms : 2010 net assigned charge : 10.50002 assigned positive charge : 314.0828 centred at (gu) : 91.59154 86.22452 87.55740 assigned negative charge : -303.5833 centred at (gu) : 91.47890 86.47221 87.69238 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20069 grid for indexing accessible points = 1.400000 m= 23351 mr = 43769 m= 3944 mr = 16679 m= 275 mr = 2246 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 387 time to turn everything in is 0.5000000 number of dielectric boundary points 30212 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 15865 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) : 0.6476024 object centre at (A) : 25.89700 5.843000 58.43600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1641649E-02 4.1740432E-02 midg,1,midg; midg,igrid,midg 2.8899102E-02 1.2914597E-03 1,midg,midg; igrid,midg,midg 2.1739244E-02 4.9608544E-02 gauss-seidel spectral radius is 0.9986451 estimated iterations to convergence 215 setup time was (sec) 0.7900000 now iterating at: 23:25:40 rms-change max change #iterations 3.842386 175.6655 at 10iterations 1.798634 64.83527 at 20iterations 0.8469931 27.91328 at 30iterations 0.3964175 13.65387 at 40iterations 0.1859434 6.918829 at 50iterations 8.7397330E-02 3.053836 at 60iterations 4.0878832E-02 1.403269 at 70iterations 1.9238455E-02 0.6309301 at 80iterations 8.9990264E-03 0.3313541 at 90iterations 4.2246114E-03 0.1469135 at 100iterations 1.9889062E-03 6.7449570E-02 at 110iterations 9.3644310E-04 3.2402039E-02 at 120iterations finished qdiffx linear iterations at : 23:25:47 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 9.3644310E-04 3.2402039E-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 23:25:47 7.689u 0.256s 0:08.26 96.0% 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 23:25:47 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2144 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: 2.914211 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): -1.589000 53.38300 ymin,ymax (A): -15.83500 27.52100 zmin,zma (A): 32.70800 84.16400 x,y,z range (A): 54.97200 43.35600 51.45600 scale (grids/A): 2.914211 object centre (A): 25.89700 5.843000 58.43600 number of atom coordinates read : 2144 total number of charged atoms : 2010 net assigned charge : 10.50002 assigned positive charge : 314.0828 centred at (gu) : 92.38731 84.33671 86.33604 assigned negative charge : -303.5833 centred at (gu) : 92.21832 84.70839 86.53865 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 151054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20069 grid for indexing accessible points = 1.400000 m= 74606 mr = 106631 m= 27659 mr = 59609 m= 7024 mr = 21623 m= 1153 mr = 5010 m= 76 mr = 664 m= 0 mr = 28 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 1466 time to turn everything in is 1.210000 number of dielectric boundary points 68007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 16080 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) : 1.942807 object centre at (A) : 25.89700 5.843000 58.43600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1780009 0.5387696 midg,1,midg; midg,igrid,midg 0.2525836 1.9485194E-02 1,midg,midg; igrid,midg,midg 9.9658005E-02 0.5140658 gauss-seidel spectral radius is 0.9992599 estimated iterations to convergence 290 setup time was (sec) 1.550000 now iterating at: 23:25:49 rms-change max change #iterations 9.147451 500.4310 at 10iterations 5.399708 141.4476 at 20iterations 3.153391 75.19600 at 30iterations 1.838405 38.51249 at 40iterations 1.068534 24.44116 at 50iterations 0.6193758 11.85700 at 60iterations 0.3585707 7.453327 at 70iterations 0.2075310 5.064367 at 80iterations 0.1196808 2.509765 at 90iterations 6.9206633E-02 1.383230 at 100iterations 3.9905731E-02 0.7309952 at 110iterations 2.2970632E-02 0.4586487 at 120iterations 1.3240445E-02 0.2757893 at 130iterations 7.6197153E-03 0.1436844 at 140iterations 4.4012787E-03 8.1605911E-02 at 150iterations 2.5435009E-03 5.3798676E-02 at 160iterations 1.4753070E-03 3.2554626E-02 at 170iterations 8.5429015E-04 1.6012192E-02 at 180iterations finished qdiffx linear iterations at : 23:26:00 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 8.5429015E-04 1.6012192E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 23:26:01 12.573u 0.236s 0:13.08 97.8% 0+0k 0+0io 0pf+0w