Mon Oct 10 17:17:02 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 17:17:02 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2883 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! 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= 0.1100000 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 : 2735 net assigned charge : -0.6489890 assigned positive charge : 432.6852 centred at (gu) : 91.33108 89.55355 88.86033 assigned negative charge : -433.3349 centred at (gu) : 91.27251 89.60235 88.82359 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= 2605 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8845 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1140379E-09 1.2088202E-09 midg,1,midg; midg,igrid,midg 2.4555820E-09 -2.7663316E-09 1,midg,midg; igrid,midg,midg -2.6638023E-09 3.7246950E-09 gauss-seidel spectral radius is 0.9860873 estimated iterations to convergence 69 setup time was (sec) 0.7100000 now iterating at: 17:17:03 rms-change max change #iterations 0.1238060 23.35773 at 10iterations 1.0962899E-02 1.796312 at 20iterations 1.0068681E-03 0.1438313 at 30iterations 1.0679126E-04 1.9243240E-02 at 40iterations 1.8797746E-05 2.9649734E-03 at 50iterations finished qdiffx linear iterations at : 17:17:06 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.8797746E-05 2.9649734E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 17:17:07 4.273u 0.204s 0:04.79 93.3% 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 17:17:07 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2883 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! 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 : 2735 net assigned charge : -0.6489890 assigned positive charge : 432.6852 centred at (gu) : 93.99265 88.65968 86.58028 assigned negative charge : -433.3349 centred at (gu) : 93.81710 88.80650 86.47011 start vw surface at 0.2300000 fill in re-entrant regions at 0.3600000 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 = 0.3400000 no. cavity mid-points inaccessible to solvent = 221 time to turn everything in is 0.7500000 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 0.8900000 number of grid points assigned charge 21407 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 1.3652540E-02 -4.6565376E-02 midg,1,midg; midg,igrid,midg 4.3326989E-03 -6.1173626E-04 1,midg,midg; igrid,midg,midg -1.6141387E-02 1.1458741E-02 gauss-seidel spectral radius is 0.9985557 estimated iterations to convergence 209 setup time was (sec) 1.100000 now iterating at: 17:17:08 rms-change max change #iterations 4.164830 183.9633 at 10iterations 1.905150 75.79468 at 20iterations 0.8739093 30.80181 at 30iterations 0.3993516 12.98226 at 40iterations 0.1822853 5.699032 at 50iterations 8.3658218E-02 2.803383 at 60iterations 3.8349792E-02 1.179277 at 70iterations 1.7555397E-02 0.5526990 at 80iterations 8.0378270E-03 0.2495168 at 90iterations 3.6807491E-03 0.1161766 at 100iterations 1.6905189E-03 5.5984974E-02 at 110iterations 7.7732722E-04 2.3967743E-02 at 120iterations finished qdiffx linear iterations at : 17:17:17 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 7.7732722E-04 2.3967743E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 17:17:17 9.552u 0.250s 0:10.22 95.8% 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 17:17:17 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2883 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! 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 : 2735 net assigned charge : -0.6489890 assigned positive charge : 432.6852 centred at (gu) : 95.98872 87.98930 84.87013 assigned negative charge : -433.3349 centred at (gu) : 95.72561 88.20962 84.70502 start vw surface at 0.1800000 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 = 1.050000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.780000 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 1.950000 number of grid points assigned charge 21876 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 0.3417728 -1.002828 midg,1,midg; midg,igrid,midg 2.6828965E-02 -1.1768109E-02 1,midg,midg; igrid,midg,midg -9.4199575E-02 0.1931112 gauss-seidel spectral radius is 0.9992493 estimated iterations to convergence 288 setup time was (sec) 2.160000 now iterating at: 17:17:20 rms-change max change #iterations 10.14193 339.4834 at 10iterations 5.972404 137.1629 at 20iterations 3.492504 78.27849 at 30iterations 2.032477 44.76221 at 40iterations 1.180603 23.86127 at 50iterations 0.6818467 13.25767 at 60iterations 0.3930904 7.269722 at 70iterations 0.2268090 4.370974 at 80iterations 0.1304513 2.752411 at 90iterations 7.4883066E-02 1.356038 at 100iterations 4.3023478E-02 0.8474770 at 110iterations 2.4707876E-02 0.4354515 at 120iterations 1.4162888E-02 0.2619886 at 130iterations 8.1395647E-03 0.1613464 at 140iterations 4.6638129E-03 8.2460403E-02 at 150iterations 2.6725710E-03 4.8637390E-02 at 160iterations 1.5327994E-03 2.7775764E-02 at 170iterations 8.7977905E-04 1.6489029E-02 at 180iterations finished qdiffx linear iterations at : 17:17:33 total time elapsed so far: 15.20000 # loops : 180 mean,max change (kT/e) : 8.7977905E-04 1.6489029E-02 energy calculations done at 15.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.46000 DelPhi exited at 17:17:34 15.459u 0.261s 0:16.94 92.7% 0+0k 0+0io 0pf+0w