Sat Oct 15 11:27:40 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 Sat Oct 15 2011 at 11:27:40 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3397 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: 0.5785608 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): -2.097000 53.58700 ymin,ymax (A): -18.41200 37.95600 zmin,zma (A): -6.097000 55.43500 x,y,z range (A): 55.68400 56.36800 61.53200 scale (grids/A): 0.5785608 object centre (A): 25.74500 9.772001 24.66900 number of atom coordinates read : 3397 total number of charged atoms : 3251 net assigned charge : -4.999964 assigned positive charge : 506.6696 centred at (gu) : 89.95860 87.72103 90.69033 assigned negative charge : -511.6708 centred at (gu) : 90.00581 87.70006 90.67165 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7530 nv = 96 ne = 84 npr = 68950 no. pairs analyzed = 68950 no. exposed pairs = 4329 no. arc points = 30106 no. surface atoms = 1452 nbur = 1945 mkacc time = 0.1100000 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 = 1.484000 m= 311 mr = 4027 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3017 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9581 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2567378E-09 -6.6982681E-10 midg,1,midg; midg,igrid,midg -2.6057907E-09 -3.2068390E-10 1,midg,midg; igrid,midg,midg 1.0482927E-10 -2.1419944E-09 gauss-seidel spectral radius is 0.9846159 estimated iterations to convergence 66 setup time was (sec) 0.4500000 now iterating at: 11:27:40 rms-change max change #iterations 0.1024978 16.21034 at 10iterations 8.1760352E-03 1.092152 at 20iterations 7.2468055E-04 0.1114998 at 30iterations 1.1247818E-04 2.2941589E-02 at 40iterations 2.9469335E-05 5.3467751E-03 at 50iterations finished qdiffx linear iterations at : 11:27:44 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 2.9469335E-05 5.3467751E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 11:27:44 3.574u 0.255s 0:04.39 87.0% 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 15 2011 at 11:27:44 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3397 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: 1.735682 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): -2.097000 53.58700 ymin,ymax (A): -18.41200 37.95600 zmin,zma (A): -6.097000 55.43500 x,y,z range (A): 55.68400 56.36800 61.53200 scale (grids/A): 1.735682 object centre (A): 25.74500 9.772001 24.66900 number of atom coordinates read : 3397 total number of charged atoms : 3251 net assigned charge : -4.999964 assigned positive charge : 506.6696 centred at (gu) : 89.87487 83.16205 92.06983 assigned negative charge : -511.6708 centred at (gu) : 90.01727 83.09991 92.01450 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30106 grid for indexing accessible points = 1.400000 m= 27503 mr = 57000 m= 3245 mr = 19338 m= 102 mr = 1642 m= 2 mr = 14 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 35401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 25224 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) : 0.5785608 object centre at (A) : 25.74500 9.772001 24.66900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3427099E-04 -5.1504308E-03 midg,1,midg; midg,igrid,midg -2.4431594E-02 -6.2190497E-06 1,midg,midg; igrid,midg,midg -1.1184431E-02 -4.5470703E-02 gauss-seidel spectral radius is 0.9984419 estimated iterations to convergence 201 setup time was (sec) 0.6400000 now iterating at: 11:27:45 rms-change max change #iterations 4.076163 193.1243 at 10iterations 1.807217 62.70654 at 20iterations 0.8008862 26.40577 at 30iterations 0.3574880 10.66744 at 40iterations 0.1591527 5.057507 at 50iterations 7.0441775E-02 2.196798 at 60iterations 3.1492863E-02 0.9647567 at 70iterations 1.4010862E-02 0.4411888 at 80iterations 6.2595992E-03 0.2299500 at 90iterations 2.8177379E-03 9.5146179E-02 at 100iterations 1.2764424E-03 4.0176392E-02 at 110iterations 5.9024448E-04 1.8545151E-02 at 120iterations finished qdiffx linear iterations at : 11:27:53 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 5.9024448E-04 1.8545151E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 11:27:53 8.304u 0.267s 0:09.32 91.8% 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 Sat Oct 15 2011 at 11:27:54 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3397 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: 2.603523 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): -2.097000 53.58700 ymin,ymax (A): -18.41200 37.95600 zmin,zma (A): -6.097000 55.43500 x,y,z range (A): 55.68400 56.36800 61.53200 scale (grids/A): 2.603523 object centre (A): 25.74500 9.772001 24.66900 number of atom coordinates read : 3397 total number of charged atoms : 3251 net assigned charge : -4.999964 assigned positive charge : 506.6696 centred at (gu) : 89.81200 79.74291 93.10455 assigned negative charge : -511.6708 centred at (gu) : 90.02575 79.64962 93.02162 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 191279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30106 grid for indexing accessible points = 1.400000 m= 92688 mr = 138410 m= 28586 mr = 74412 m= 5349 mr = 21747 m= 430 mr = 3576 m= 8 mr = 168 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 80027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 25996 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) : 1.735682 object centre at (A) : 25.74500 9.772001 24.66900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7448559E-02 8.7360851E-02 midg,1,midg; midg,igrid,midg -0.3414295 -8.0039874E-03 1,midg,midg; igrid,midg,midg -0.1995333 -0.7736518 gauss-seidel spectral radius is 0.9992250 estimated iterations to convergence 284 setup time was (sec) 1.330000 now iterating at: 11:27:55 rms-change max change #iterations 10.20233 304.9166 at 10iterations 5.906163 134.9827 at 20iterations 3.397302 72.19086 at 30iterations 1.953186 37.19495 at 40iterations 1.116813 21.93709 at 50iterations 0.6380758 11.95691 at 60iterations 0.3636523 6.762423 at 70iterations 0.2070499 3.814001 at 80iterations 0.1179097 2.308151 at 90iterations 6.7053266E-02 1.154930 at 100iterations 3.8084116E-02 0.6500301 at 110iterations 2.1612054E-02 0.3860655 at 120iterations 1.2302822E-02 0.2440605 at 130iterations 7.0071113E-03 0.1228619 at 140iterations 4.0147784E-03 7.1978092E-02 at 150iterations 2.3021232E-03 3.9755344E-02 at 160iterations 1.3373268E-03 2.5094226E-02 at 170iterations 7.9217361E-04 1.7731667E-02 at 180iterations finished qdiffx linear iterations at : 11:28:08 total time elapsed so far: 14.29000 # loops : 180 mean,max change (kT/e) : 7.9217361E-04 1.7731667E-02 energy calculations done at 14.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.43000 DelPhi exited at 11:28:09 14.429u 0.253s 0:15.25 96.1% 0+0k 0+0io 0pf+0w