Sat Oct 8 11:44:52 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 11:44:52 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 = 4447 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: 0.5295807 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): 59.16500 114.6770 ymin,ymax (A): 19.09800 86.32100 zmin,zma (A): -7.708000 55.57300 x,y,z range (A): 55.51200 67.22300 63.28100 scale (grids/A): 0.5295807 object centre (A): 86.92100 52.70950 23.93250 number of atom coordinates read : 4447 total number of charged atoms : 4288 net assigned charge : -4.499950 assigned positive charge : 666.9420 centred at (gu) : 90.06583 89.19408 89.54535 assigned negative charge : -671.4453 centred at (gu) : 90.27618 89.14221 89.46704 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7860 nv = 96 ne = 84 npr = 93284 no. pairs analyzed = 93284 no. exposed pairs = 4992 no. arc points = 34423 no. surface atoms = 1688 nbur = 2759 mkacc time = 0.1600000 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 = 1.624000 m= 299 mr = 4515 m= 0 mr = 11 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 76 time to turn everything in is 0.3000000 number of dielectric boundary points 3633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3526 ## 520 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10589 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2857619E-10 2.4442390E-10 midg,1,midg; midg,igrid,midg -5.1137844E-10 1.1021711E-10 1,midg,midg; igrid,midg,midg 9.3752228E-10 -1.3121566E-09 gauss-seidel spectral radius is 0.9817272 estimated iterations to convergence 61 setup time was (sec) 0.5000000 now iterating at: 11:44:53 rms-change max change #iterations 7.8005016E-02 14.70389 at 10iterations 5.3723631E-03 0.7844830 at 20iterations 6.6067150E-04 9.7105026E-02 at 30iterations 1.6854877E-04 2.3665637E-02 at 40iterations 5.3075575E-05 8.0356598E-03 at 50iterations finished qdiffx linear iterations at : 11:44:56 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 5.3075575E-05 8.0356598E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 11:44:57 3.703u 0.214s 0:04.29 91.1% 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 Sat Oct 8 2011 at 11:44:57 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 = 4447 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.588742 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): 59.16500 114.6770 ymin,ymax (A): 19.09800 86.32100 zmin,zma (A): -7.708000 55.57300 x,y,z range (A): 55.51200 67.22300 63.28100 scale (grids/A): 1.588742 object centre (A): 86.92100 52.70950 23.93250 number of atom coordinates read : 4447 total number of charged atoms : 4288 net assigned charge : -4.499950 assigned positive charge : 666.9420 centred at (gu) : 90.19604 87.58090 88.63493 assigned negative charge : -671.4453 centred at (gu) : 90.82809 87.42578 88.40085 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34423 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 27497 mr = 64060 m= 2646 mr = 19532 m= 46 mr = 1429 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5791 time to turn everything in is 0.4400000 number of dielectric boundary points 34134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 459 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 32630 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) : 0.5295807 object centre at (A) : 86.92100 52.70950 23.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0526681E-02 7.8708160E-04 midg,1,midg; midg,igrid,midg -2.4068827E-02 1.3023227E-02 1,midg,midg; igrid,midg,midg 2.0820584E-02 -2.1507919E-02 gauss-seidel spectral radius is 0.9982147 estimated iterations to convergence 188 setup time was (sec) 0.6800000 now iterating at: 11:44:58 rms-change max change #iterations 3.956450 149.3575 at 10iterations 1.661881 52.13130 at 20iterations 0.6990182 23.11642 at 30iterations 0.2937594 9.627411 at 40iterations 0.1238942 4.293957 at 50iterations 5.2374743E-02 1.814323 at 60iterations 2.2092190E-02 0.7066218 at 70iterations 9.3617225E-03 0.2812567 at 80iterations 3.9952169E-03 0.1234870 at 90iterations 1.7387314E-03 5.8849096E-02 at 100iterations 7.8375003E-04 2.6485443E-02 at 110iterations 3.7832590E-04 1.2358665E-02 at 120iterations finished qdiffx linear iterations at : 11:45:06 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 3.7832590E-04 1.2358665E-02 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 11:45:06 8.468u 0.231s 0:09.48 91.6% 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 11:45:06 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 = 4447 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: 2.383113 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): 59.16500 114.6770 ymin,ymax (A): 19.09800 86.32100 zmin,zma (A): -7.708000 55.57300 x,y,z range (A): 55.51200 67.22300 63.28100 scale (grids/A): 2.383113 object centre (A): 86.92100 52.70950 23.93250 number of atom coordinates read : 4447 total number of charged atoms : 4288 net assigned charge : -4.499950 assigned positive charge : 666.9420 centred at (gu) : 90.29368 86.37099 87.95198 assigned negative charge : -671.4453 centred at (gu) : 91.24207 86.13855 87.60117 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 207268 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34423 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 97043 mr = 155745 m= 26578 mr = 79109 m= 4113 mr = 20482 m= 233 mr = 2871 m= 4 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 19847 time to turn everything in is 1.140000 number of dielectric boundary points 76942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 34252 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) : 1.588742 object centre at (A) : 86.92100 52.70950 23.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3450221 6.1591364E-02 midg,1,midg; midg,igrid,midg -0.8167712 0.1577807 1,midg,midg; igrid,midg,midg 0.3539703 -0.3121683 gauss-seidel spectral radius is 0.9991691 estimated iterations to convergence 274 setup time was (sec) 1.480000 now iterating at: 11:45:08 rms-change max change #iterations 10.32178 392.8123 at 10iterations 5.878477 129.0499 at 20iterations 3.320643 103.2780 at 30iterations 1.872719 40.02782 at 40iterations 1.053566 22.38754 at 50iterations 0.5905725 13.04624 at 60iterations 0.3307376 6.503872 at 70iterations 0.1848272 3.512718 at 80iterations 0.1034242 1.905493 at 90iterations 5.7552539E-02 1.203896 at 100iterations 3.2152973E-02 0.6048412 at 110iterations 1.7954836E-02 0.3061171 at 120iterations 1.0001958E-02 0.1712379 at 130iterations 5.6022382E-03 0.1067734 at 140iterations 3.1531511E-03 5.8359146E-02 at 150iterations 1.7862326E-03 3.2455444E-02 at 160iterations 1.0268170E-03 1.7982483E-02 at 170iterations 6.0676521E-04 1.1129379E-02 at 180iterations finished qdiffx linear iterations at : 11:45:23 total time elapsed so far: 16.88000 # loops : 180 mean,max change (kT/e) : 6.0676521E-04 1.1129379E-02 energy calculations done at 16.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.02000 DelPhi exited at 11:45:24 17.022u 0.345s 0:17.86 97.2% 0+0k 0+0io 0pf+0w