Mon Oct 10 17:16:31 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 Mon Oct 10 2011 at 17:16:31 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 = 2883 !!! WARNING: ASN 315 has a net charge of -0.0550 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: 0.6093699 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): -33.34300 23.57900 ymin,ymax (A): 40.24400 89.64400 zmin,zma (A): 0.4210001 58.84200 x,y,z range (A): 56.92200 49.39999 58.42100 scale (grids/A): 0.6093699 object centre (A): -4.882001 64.94400 29.63150 number of atom coordinates read : 2883 total number of charged atoms : 2739 net assigned charge : -0.5549893 assigned positive charge : 430.6452 centred at (gu) : 91.34048 89.54820 88.84027 assigned negative charge : -431.2009 centred at (gu) : 91.28431 89.59756 88.80440 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7136 nv = 96 ne = 84 npr = 57367 no. pairs analyzed = 57367 no. exposed pairs = 3926 no. arc points = 26593 no. surface atoms = 1318 nbur = 1565 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3746 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2609 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8853 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9827272E-09 1.2034463E-09 midg,1,midg; midg,igrid,midg 2.5381488E-09 -2.7278826E-09 1,midg,midg; igrid,midg,midg -2.5085343E-09 3.6125896E-09 gauss-seidel spectral radius is 0.9860873 estimated iterations to convergence 69 setup time was (sec) 0.7100000 now iterating at: 17:16:32 rms-change max change #iterations 0.1216532 22.84216 at 10iterations 1.0751621E-02 1.668783 at 20iterations 9.9844125E-04 0.1341286 at 30iterations 1.0913135E-04 1.9847870E-02 at 40iterations 2.0041529E-05 3.1394958E-03 at 50iterations finished qdiffx linear iterations at : 17:16:35 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 2.0041529E-05 3.1394958E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 17:16:35 4.312u 0.193s 0:04.79 93.9% 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 17:16:36 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 = 2883 !!! WARNING: ASN 315 has a net charge of -0.0550 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: 1.828110 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): -33.34300 23.57900 ymin,ymax (A): 40.24400 89.64400 zmin,zma (A): 0.4210001 58.84200 x,y,z range (A): 56.92200 49.39999 58.42100 scale (grids/A): 1.828110 object centre (A): -4.882001 64.94400 29.63150 number of atom coordinates read : 2883 total number of charged atoms : 2739 net assigned charge : -0.5549893 assigned positive charge : 430.6452 centred at (gu) : 94.02090 88.64355 86.52014 assigned negative charge : -431.2009 centred at (gu) : 93.85247 88.79214 86.41251 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 77627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26593 grid for indexing accessible points = 1.400000 m= 26090 mr = 52580 m= 3702 mr = 18319 m= 148 mr = 2087 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 221 time to turn everything in is 0.7300000 number of dielectric boundary points 34560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21439 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) : 0.6093699 object centre at (A) : -4.882001 64.94400 29.63150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3798052E-02 -4.6406943E-02 midg,1,midg; midg,igrid,midg 4.9419240E-03 -1.6513416E-04 1,midg,midg; igrid,midg,midg -1.6146550E-02 1.0962955E-02 gauss-seidel spectral radius is 0.9985557 estimated iterations to convergence 209 setup time was (sec) 1.090000 now iterating at: 17:16:37 rms-change max change #iterations 4.132156 183.9633 at 10iterations 1.890205 74.49585 at 20iterations 0.8670520 30.80182 at 30iterations 0.3961203 12.92573 at 40iterations 0.1809045 5.708786 at 50iterations 8.2997769E-02 2.718031 at 60iterations 3.8070355E-02 1.205545 at 70iterations 1.7420765E-02 0.5711317 at 80iterations 7.9755653E-03 0.2436579 at 90iterations 3.6534970E-03 0.1181469 at 100iterations 1.6777094E-03 5.3191185E-02 at 110iterations 7.7201729E-04 2.4139404E-02 at 120iterations finished qdiffx linear iterations at : 17:16:45 total time elapsed so far: 9.290000 # loops : 120 mean,max change (kT/e) : 7.7201729E-04 2.4139404E-02 energy calculations done at 9.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 17:16:46 9.535u 0.227s 0:10.19 95.6% 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 Mon Oct 10 2011 at 17:16:46 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 = 2883 !!! WARNING: ASN 315 has a net charge of -0.0550 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: 2.742165 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): -33.34300 23.57900 ymin,ymax (A): 40.24400 89.64400 zmin,zma (A): 0.4210001 58.84200 x,y,z range (A): 56.92200 49.39999 58.42100 scale (grids/A): 2.742165 object centre (A): -4.882001 64.94400 29.63150 number of atom coordinates read : 2883 total number of charged atoms : 2739 net assigned charge : -0.5549893 assigned positive charge : 430.6452 centred at (gu) : 96.03109 87.96514 84.77994 assigned negative charge : -431.2009 centred at (gu) : 95.77867 88.18807 84.61861 start vw surface at 0.1900000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 179834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26593 grid for indexing accessible points = 1.400000 m= 86146 mr = 128178 m= 29029 mr = 68367 m= 6419 mr = 22684 m= 658 mr = 4600 m= 22 mr = 336 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.770000 number of dielectric boundary points 77943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 21908 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) : 1.828110 object centre at (A) : -4.882001 64.94400 29.63150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3434519 -1.000730 midg,1,midg; midg,igrid,midg 3.4771446E-02 -5.4355613E-03 1,midg,midg; igrid,midg,midg -9.4837956E-02 0.1868941 gauss-seidel spectral radius is 0.9992493 estimated iterations to convergence 288 setup time was (sec) 2.160000 now iterating at: 17:16:48 rms-change max change #iterations 10.07508 339.4834 at 10iterations 5.934690 136.5626 at 20iterations 3.471566 78.23270 at 30iterations 2.020955 44.28367 at 40iterations 1.173955 23.52788 at 50iterations 0.6782903 13.35849 at 60iterations 0.3910486 6.969925 at 70iterations 0.2256110 4.361944 at 80iterations 0.1297910 2.745255 at 90iterations 7.4502803E-02 1.364162 at 100iterations 4.2811573E-02 0.8283195 at 110iterations 2.4586072E-02 0.4306049 at 120iterations 1.4095947E-02 0.2649422 at 130iterations 8.1009045E-03 0.1626205 at 140iterations 4.6422821E-03 8.2832336E-02 at 150iterations 2.6613770E-03 4.8492432E-02 at 160iterations 1.5264866E-03 2.7940750E-02 at 170iterations 8.7657600E-04 1.6297340E-02 at 180iterations finished qdiffx linear iterations at : 17:17:01 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 8.7657600E-04 1.6297340E-02 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.47000 DelPhi exited at 17:17:02 15.473u 0.273s 0:16.06 98.0% 0+0k 0+0io 0pf+0w