Sat Oct 15 12:33:28 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 15 2011 at 12:33:28 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 = 1650 !!! WARNING: MN4 436 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7530088 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): 6.383000 51.14300 ymin,ymax (A): 15.49100 62.76800 zmin,zma (A): -8.665000 36.63300 x,y,z range (A): 44.76000 47.27700 45.29800 scale (grids/A): 0.7530088 object centre (A): 28.76300 39.12950 13.98400 number of atom coordinates read : 1650 total number of charged atoms : 1513 net assigned charge : -8.099994 assigned positive charge : 241.4202 centred at (gu) : 90.21519 88.62171 89.64397 assigned negative charge : -249.5201 centred at (gu) : 90.26334 88.29324 90.12031 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6362 nv = 96 ne = 84 npr = 35498 no. pairs analyzed = 35498 no. exposed pairs = 2084 no. arc points = 14692 no. surface atoms = 711 nbur = 939 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 3554 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2300000 number of dielectric boundary points 3173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1128 ## 70 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0497239E-07 -6.4939104E-07 midg,1,midg; midg,igrid,midg -6.8584791E-07 1.0883898E-07 1,midg,midg; igrid,midg,midg -1.2871553E-07 -2.4146519E-07 gauss-seidel spectral radius is 0.9907587 estimated iterations to convergence 84 setup time was (sec) 0.5700000 now iterating at: 12:33:29 rms-change max change #iterations 0.2309842 76.92047 at 10iterations 3.1686939E-02 7.413635 at 20iterations 4.3881740E-03 0.7229614 at 30iterations 6.0945813E-04 8.2330704E-02 at 40iterations 8.4849897E-05 1.2641907E-02 at 50iterations finished qdiffx linear iterations at : 12:33:33 total time elapsed so far: 5.030000 # loops : 50 mean,max change (kT/e) : 8.4849897E-05 1.2641907E-02 energy calculations done at 5.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.200000 DelPhi exited at 12:33:34 5.203u 0.471s 0:05.99 94.6% 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 Sat Oct 15 2011 at 12:33:34 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 = 1650 !!! WARNING: MN4 436 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.259027 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): 6.383000 51.14300 ymin,ymax (A): 15.49100 62.76800 zmin,zma (A): -8.665000 36.63300 x,y,z range (A): 44.76000 47.27700 45.29800 scale (grids/A): 2.259027 object centre (A): 28.76300 39.12950 13.98400 number of atom coordinates read : 1650 total number of charged atoms : 1513 net assigned charge : -8.099994 assigned positive charge : 241.4202 centred at (gu) : 90.64577 85.86503 88.93211 assigned negative charge : -249.5201 centred at (gu) : 90.79002 84.87968 90.36111 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14692 grid for indexing accessible points = 1.400000 m= 26738 mr = 45415 m= 5513 mr = 20791 m= 513 mr = 3876 m= 12 mr = 277 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1138 time to turn everything in is 0.6100000 number of dielectric boundary points 28772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 12066 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) : 0.7530088 object centre at (A) : 28.76300 39.12950 13.98400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2635144E-02 -0.1079860 midg,1,midg; midg,igrid,midg -0.1004869 3.3369556E-02 1,midg,midg; igrid,midg,midg -6.2436551E-02 -6.4635150E-02 gauss-seidel spectral radius is 0.9989119 estimated iterations to convergence 240 setup time was (sec) 0.9900000 now iterating at: 12:33:35 rms-change max change #iterations 4.573915 247.9770 at 10iterations 2.317660 141.0328 at 20iterations 1.169131 42.52552 at 30iterations 0.5970587 24.21973 at 40iterations 0.3027261 9.694611 at 50iterations 0.1540326 4.852831 at 60iterations 7.7953167E-02 2.342113 at 70iterations 3.9692141E-02 1.239085 at 80iterations 2.0081855E-02 0.6656570 at 90iterations 1.0200603E-02 0.2992859 at 100iterations 5.1778574E-03 0.1626867 at 110iterations 2.6322124E-03 8.0654144E-02 at 120iterations finished qdiffx linear iterations at : 12:33:47 total time elapsed so far: 12.60000 # loops : 120 mean,max change (kT/e) : 2.6322124E-03 8.0654144E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 12:33:47 12.775u 0.502s 0:13.53 98.0% 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 12:33:47 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 = 1650 !!! WARNING: MN4 436 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.388540 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): 6.383000 51.14300 ymin,ymax (A): 15.49100 62.76800 zmin,zma (A): -8.665000 36.63300 x,y,z range (A): 44.76000 47.27700 45.29800 scale (grids/A): 3.388540 object centre (A): 28.76300 39.12950 13.98400 number of atom coordinates read : 1650 total number of charged atoms : 1513 net assigned charge : -8.099994 assigned positive charge : 241.4202 centred at (gu) : 90.96861 83.79758 88.39814 assigned negative charge : -249.5201 centred at (gu) : 91.18501 82.31956 90.54171 start vw surface at 0.1000000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 152639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14692 grid for indexing accessible points = 1.400000 m= 81589 mr = 109334 m= 35469 mr = 68256 m= 10523 mr = 29948 m= 2121 mr = 8394 m= 283 mr = 1619 m= 22 mr = 211 m= 0 mr = 15 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 3983 time to turn everything in is 1.840000 number of dielectric boundary points 64869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 12104 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) : 2.259027 object centre at (A) : 28.76300 39.12950 13.98400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4672986 -0.6822225 midg,1,midg; midg,igrid,midg -0.9039466 0.3381769 1,midg,midg; igrid,midg,midg -0.3801292 -0.4529175 gauss-seidel spectral radius is 0.9993119 estimated iterations to convergence 301 setup time was (sec) 2.220000 now iterating at: 12:33:50 rms-change max change #iterations 9.801929 617.4471 at 10iterations 5.734563 145.4670 at 20iterations 3.352077 76.91062 at 30iterations 1.965257 55.00828 at 40iterations 1.147237 20.21763 at 50iterations 0.6713936 14.59058 at 60iterations 0.3931112 6.667725 at 70iterations 0.2301978 4.234191 at 80iterations 0.1343063 2.223873 at 90iterations 7.8841485E-02 1.312285 at 100iterations 4.6083432E-02 0.8431387 at 110iterations 2.6994973E-02 0.4542389 at 120iterations 1.5773980E-02 0.3058834 at 130iterations 9.2259943E-03 0.1676722 at 140iterations 5.3937924E-03 9.0648651E-02 at 150iterations 3.1651920E-03 5.4210186E-02 at 160iterations 1.8524313E-03 3.5763741E-02 at 170iterations 1.0811592E-03 1.9878387E-02 at 180iterations finished qdiffx linear iterations at : 12:34:09 total time elapsed so far: 21.09000 # loops : 180 mean,max change (kT/e) : 1.0811592E-03 1.9878387E-02 energy calculations done at 21.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.26000 DelPhi exited at 12:34:09 21.269u 0.564s 0:22.14 98.5% 0+0k 0+0io 0pf+0w