Sat Oct 8 17:00:00 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 17:00:00 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 = 3629 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: 0.5397211 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): 20.80400 83.99400 ymin,ymax (A): -18.05200 40.04700 zmin,zma (A): 77.68200 143.6420 x,y,z range (A): 63.18999 58.09900 65.96000 scale (grids/A): 0.5397211 object centre (A): 52.39900 10.99750 110.6620 number of atom coordinates read : 3629 total number of charged atoms : 3481 net assigned charge : -6.999982 assigned positive charge : 549.0729 centred at (gu) : 89.73432 90.44743 90.19370 assigned negative charge : -556.0748 centred at (gu) : 89.79370 90.42563 90.18236 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6643 nv = 96 ne = 84 npr = 74554 no. pairs analyzed = 74554 no. exposed pairs = 4657 no. arc points = 31168 no. surface atoms = 1562 nbur = 2067 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 = 1.596000 m= 272 mr = 3450 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3101 ## 359 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8851 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9756090E-10 -2.8075045E-10 midg,1,midg; midg,igrid,midg -4.3525417E-10 -2.2178689E-10 1,midg,midg; igrid,midg,midg 4.8781069E-11 -6.8808603E-10 gauss-seidel spectral radius is 0.9823467 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 17:00:01 rms-change max change #iterations 7.6311640E-02 12.64937 at 10iterations 5.0911116E-03 0.7718983 at 20iterations 4.7283448E-04 7.4924469E-02 at 30iterations 1.0338162E-04 1.7097473E-02 at 40iterations 3.1095209E-05 4.8682690E-03 at 50iterations finished qdiffx linear iterations at : 17:00:03 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 3.1095209E-05 4.8682690E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 17:00:04 3.180u 0.141s 0:03.60 92.2% 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 17:00:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3629 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: 1.619163 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): 20.80400 83.99400 ymin,ymax (A): -18.05200 40.04700 zmin,zma (A): 77.68200 143.6420 x,y,z range (A): 63.18999 58.09900 65.96000 scale (grids/A): 1.619163 object centre (A): 52.39900 10.99750 110.6620 number of atom coordinates read : 3629 total number of charged atoms : 3481 net assigned charge : -6.999982 assigned positive charge : 549.0729 centred at (gu) : 89.20188 91.34123 90.57993 assigned negative charge : -556.0748 centred at (gu) : 89.38077 91.27626 90.54673 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31168 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23274 mr = 50255 m= 2400 mr = 15788 m= 54 mr = 1081 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 32109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 26579 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) : 0.5397211 object centre at (A) : 52.39900 10.99750 110.6620 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8142547E-03 -1.1622114E-05 midg,1,midg; midg,igrid,midg -4.3789963E-03 1.2152202E-03 1,midg,midg; igrid,midg,midg -1.0493498E-02 -2.7448889E-02 gauss-seidel spectral radius is 0.9982095 estimated iterations to convergence 188 setup time was (sec) 0.7800000 now iterating at: 17:00:05 rms-change max change #iterations 3.668782 167.6243 at 10iterations 1.535506 57.98483 at 20iterations 0.6443937 26.21017 at 30iterations 0.2708220 9.738081 at 40iterations 0.1143360 4.293839 at 50iterations 4.7960978E-02 1.612411 at 60iterations 2.0312119E-02 0.6860567 at 70iterations 8.6540338E-03 0.2993622 at 80iterations 3.7424657E-03 0.1400337 at 90iterations 1.6819921E-03 5.5200607E-02 at 100iterations 8.1417238E-04 3.1158447E-02 at 110iterations 4.3724151E-04 1.4497757E-02 at 120iterations finished qdiffx linear iterations at : 17:00:11 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 4.3724151E-04 1.4497757E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 17:00:11 6.999u 0.168s 0:07.45 95.9% 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 Sat Oct 8 2011 at 17:00:11 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 = 3629 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: 2.428745 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): 20.80400 83.99400 ymin,ymax (A): -18.05200 40.04700 zmin,zma (A): 77.68200 143.6420 x,y,z range (A): 63.18999 58.09900 65.96000 scale (grids/A): 2.428745 object centre (A): 52.39900 10.99750 110.6620 number of atom coordinates read : 3629 total number of charged atoms : 3481 net assigned charge : -6.999982 assigned positive charge : 549.0729 centred at (gu) : 88.80264 92.01151 90.86974 assigned negative charge : -556.0748 centred at (gu) : 89.07113 91.91421 90.82001 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 170590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31168 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 80060 mr = 123038 m= 22890 mr = 62499 m= 3755 mr = 17047 m= 226 mr = 2297 m= 9 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 72581 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 27809 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) : 1.619163 object centre at (A) : 52.39900 10.99750 110.6620 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2643721E-03 2.6106185E-03 midg,1,midg; midg,igrid,midg -9.3299247E-02 3.9108531E-03 1,midg,midg; igrid,midg,midg -0.2591062 -0.3956251 gauss-seidel spectral radius is 0.9991562 estimated iterations to convergence 272 setup time was (sec) 1.560000 now iterating at: 17:00:13 rms-change max change #iterations 9.638610 338.6749 at 10iterations 5.476968 129.7729 at 20iterations 3.105328 77.94976 at 30iterations 1.746367 36.54750 at 40iterations 0.9768274 20.20379 at 50iterations 0.5453241 10.40827 at 60iterations 0.3044029 6.235428 at 70iterations 0.1694399 3.587143 at 80iterations 9.4242387E-02 1.771887 at 90iterations 5.2290805E-02 0.9549732 at 100iterations 2.9044613E-02 0.6119537 at 110iterations 1.6096551E-02 0.3134208 at 120iterations 8.9151785E-03 0.1588249 at 130iterations 4.9570906E-03 9.1728210E-02 at 140iterations 2.7485560E-03 5.1280975E-02 at 150iterations 1.5293311E-03 2.8877258E-02 at 160iterations 8.5347105E-04 1.5420318E-02 at 170iterations 4.8046184E-04 9.8152161E-03 at 180iterations finished qdiffx linear iterations at : 17:00:23 total time elapsed so far: 11.10000 # loops : 180 mean,max change (kT/e) : 4.8046184E-04 9.8152161E-03 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 17:00:23 11.282u 0.172s 0:11.74 97.5% 0+0k 0+0io 0pf+0w