Mon Oct 10 17:13:51 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 17:13:51 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3561 !!! WARNING: HIR 201 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5892869 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): -20.05800 40.35400 ymin,ymax (A): -30.30300 27.89900 zmin,zma (A): 6.118000 65.63900 x,y,z range (A): 60.41200 58.20200 59.52100 scale (grids/A): 0.5892869 object centre (A): 10.14800 -1.202000 35.87850 number of atom coordinates read : 3561 total number of charged atoms : 3422 net assigned charge : 8.514019 assigned positive charge : 549.6188 centred at (gu) : 88.12494 90.33770 89.77228 assigned negative charge : -541.1066 centred at (gu) : 88.10987 90.32986 89.81758 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8061 nv = 96 ne = 84 npr = 72097 no. pairs analyzed = 72097 no. exposed pairs = 4462 no. arc points = 31493 no. surface atoms = 1481 nbur = 2080 mkacc time = 0.1200000 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= 381 mr = 4221 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2500000 number of dielectric boundary points 4185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3274 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 10313 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4051105E-09 8.6661867E-10 midg,1,midg; midg,igrid,midg 2.1064681E-09 3.0602070E-09 1,midg,midg; igrid,midg,midg 3.0472684E-09 2.0392019E-09 gauss-seidel spectral radius is 0.9851812 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 17:13:52 rms-change max change #iterations 0.1221151 17.85636 at 10iterations 9.8090246E-03 1.191612 at 20iterations 8.0640835E-04 0.1187630 at 30iterations 6.7428802E-05 9.0751648E-03 at 40iterations 5.5543924E-06 7.2860718E-04 at 50iterations finished qdiffx linear iterations at : 17:13:55 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 5.5543924E-06 7.2860718E-04 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 17:13:56 3.755u 0.179s 0:04.29 91.3% 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 17:13:56 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3561 !!! WARNING: HIR 201 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.767861 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): -20.05800 40.35400 ymin,ymax (A): -30.30300 27.89900 zmin,zma (A): 6.118000 65.63900 x,y,z range (A): 60.41200 58.20200 59.52100 scale (grids/A): 1.767861 object centre (A): 10.14800 -1.202000 35.87850 number of atom coordinates read : 3561 total number of charged atoms : 3422 net assigned charge : 8.514019 assigned positive charge : 549.6188 centred at (gu) : 84.37413 91.01221 89.31620 assigned negative charge : -541.1066 centred at (gu) : 84.32916 90.98940 89.45217 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31493 grid for indexing accessible points = 1.400000 m= 29787 mr = 59525 m= 4089 mr = 20945 m= 206 mr = 2289 m= 0 mr = 39 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 685 time to turn everything in is 0.4200000 number of dielectric boundary points 38598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 26592 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) : 0.5892869 object centre at (A) : 10.14800 -1.202000 35.87850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1159399E-02 3.4329809E-02 midg,1,midg; midg,igrid,midg 4.7736857E-03 3.6382940E-02 1,midg,midg; igrid,midg,midg -1.5701783E-03 2.7291764E-02 gauss-seidel spectral radius is 0.9985167 estimated iterations to convergence 206 setup time was (sec) 0.6500000 now iterating at: 17:13:57 rms-change max change #iterations 4.459546 204.7887 at 10iterations 2.006312 64.36890 at 20iterations 0.9056601 32.33033 at 30iterations 0.4123870 12.79007 at 40iterations 0.1868812 5.599342 at 50iterations 8.4596068E-02 2.677857 at 60iterations 3.8350869E-02 1.196043 at 70iterations 1.7428372E-02 0.5516663 at 80iterations 7.8745130E-03 0.2651157 at 90iterations 3.5712528E-03 0.1117477 at 100iterations 1.6200745E-03 5.0399780E-02 at 110iterations 7.3692133E-04 2.1841049E-02 at 120iterations finished qdiffx linear iterations at : 17:14:04 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 7.3692133E-04 2.1841049E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 17:14:04 7.979u 0.195s 0:08.70 93.7% 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 17:14:04 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3561 !!! WARNING: HIR 201 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.651791 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): -20.05800 40.35400 ymin,ymax (A): -30.30300 27.89900 zmin,zma (A): 6.118000 65.63900 x,y,z range (A): 60.41200 58.20200 59.52100 scale (grids/A): 2.651791 object centre (A): 10.14800 -1.202000 35.87850 number of atom coordinates read : 3561 total number of charged atoms : 3422 net assigned charge : 8.514019 assigned positive charge : 549.6188 centred at (gu) : 81.56084 91.51801 88.97388 assigned negative charge : -541.1066 centred at (gu) : 81.49359 91.48392 89.17822 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 202360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31493 grid for indexing accessible points = 1.400000 m= 97963 mr = 144870 m= 32846 mr = 78259 m= 6949 mr = 25456 m= 808 mr = 4829 m= 27 mr = 482 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 2395 time to turn everything in is 1.160000 number of dielectric boundary points 87053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 27368 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) : 1.767861 object centre at (A) : 10.14800 -1.202000 35.87850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4939667 0.4671949 midg,1,midg; midg,igrid,midg 0.1239872 0.5103986 1,midg,midg; igrid,midg,midg -0.1873159 0.5574028 gauss-seidel spectral radius is 0.9992501 estimated iterations to convergence 288 setup time was (sec) 1.450000 now iterating at: 17:14:06 rms-change max change #iterations 10.80398 309.0477 at 10iterations 6.313758 154.4865 at 20iterations 3.666866 73.21166 at 30iterations 2.119735 41.42957 at 40iterations 1.221480 25.54763 at 50iterations 0.7043411 14.19202 at 60iterations 0.4049858 7.975140 at 70iterations 0.2324073 4.347499 at 80iterations 0.1332503 2.368192 at 90iterations 7.6434925E-02 1.500336 at 100iterations 4.3811359E-02 0.7743225 at 110iterations 2.5105018E-02 0.4434972 at 120iterations 1.4363652E-02 0.2418671 at 130iterations 8.2266424E-03 0.1409073 at 140iterations 4.7125556E-03 8.5470200E-02 at 150iterations 2.6934275E-03 4.7472954E-02 at 160iterations 1.5434178E-03 2.6840210E-02 at 170iterations 8.8188617E-04 1.6531974E-02 at 180iterations finished qdiffx linear iterations at : 17:14:19 total time elapsed so far: 14.19000 # loops : 180 mean,max change (kT/e) : 8.8188617E-04 1.6531974E-02 energy calculations done at 14.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.32000 DelPhi exited at 17:14:20 14.321u 0.303s 0:15.29 95.6% 0+0k 0+0io 0pf+0w