Sun Oct 9 12:53:25 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 Sun Oct 9 2011 at 12:53:25 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 !!! WARNING: GLM 234 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6940383 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): -6.325000 41.82400 ymin,ymax (A): -14.13300 37.16100 zmin,zma (A): 2.031000 44.77400 x,y,z range (A): 48.14900 51.29400 42.74300 scale (grids/A): 0.6940383 object centre (A): 17.74950 11.51400 23.40250 number of atom coordinates read : 2405 total number of charged atoms : 2259 net assigned charge : 3.406015 assigned positive charge : 370.0330 centred at (gu) : 90.24544 91.24660 90.75880 assigned negative charge : -366.6274 centred at (gu) : 90.26757 91.40932 90.89754 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7840 nv = 96 ne = 84 npr = 47791 no. pairs analyzed = 47791 no. exposed pairs = 3040 no. arc points = 21042 no. surface atoms = 1019 nbur = 1386 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4355 m= 0 mr = 87 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2800000 number of dielectric boundary points 3911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1999 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8886 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9505411E-08 -4.4295462E-08 midg,1,midg; midg,igrid,midg 7.0852224E-08 -6.2773786E-08 1,midg,midg; igrid,midg,midg 3.0331684E-08 1.3501909E-08 gauss-seidel spectral radius is 0.9892153 estimated iterations to convergence 78 setup time was (sec) 0.5100000 now iterating at: 12:53:26 rms-change max change #iterations 0.1994366 25.85543 at 10iterations 2.4532026E-02 3.440380 at 20iterations 3.6456503E-03 0.5210571 at 30iterations 9.1475167E-04 0.1397552 at 40iterations 3.1503776E-04 4.8004150E-02 at 50iterations finished qdiffx linear iterations at : 12:53:28 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 3.1503776E-04 4.8004150E-02 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 12:53:29 3.147u 0.141s 0:03.57 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 Sun Oct 9 2011 at 12:53:29 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 !!! WARNING: GLM 234 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.082115 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): -6.325000 41.82400 ymin,ymax (A): -14.13300 37.16100 zmin,zma (A): 2.031000 44.77400 x,y,z range (A): 48.14900 51.29400 42.74300 scale (grids/A): 2.082115 object centre (A): 17.74950 11.51400 23.40250 number of atom coordinates read : 2405 total number of charged atoms : 2259 net assigned charge : 3.406015 assigned positive charge : 370.0330 centred at (gu) : 90.73582 93.73932 92.27604 assigned negative charge : -366.6274 centred at (gu) : 90.80254 94.22767 92.69227 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 83142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21042 grid for indexing accessible points = 1.400000 m= 32616 mr = 58026 m= 6222 mr = 24398 m= 552 mr = 4030 m= 14 mr = 293 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 330 time to turn everything in is 0.5800000 number of dielectric boundary points 35799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17946 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) : 0.6940383 object centre at (A) : 17.74950 11.51400 23.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1775105E-02 2.6333081E-03 midg,1,midg; midg,igrid,midg 1.9122487E-02 -5.1893942E-02 1,midg,midg; igrid,midg,midg 4.7856148E-02 -5.0071981E-03 gauss-seidel spectral radius is 0.9988291 estimated iterations to convergence 231 setup time was (sec) 0.8600000 now iterating at: 12:53:30 rms-change max change #iterations 4.907944 200.2206 at 10iterations 2.425706 77.16175 at 20iterations 1.200803 42.92212 at 30iterations 0.5941799 17.55039 at 40iterations 0.2950084 10.19701 at 50iterations 0.1465363 4.120424 at 60iterations 7.2779924E-02 2.084389 at 70iterations 3.6412522E-02 1.094090 at 80iterations 1.8268559E-02 0.5285492 at 90iterations 9.2934277E-03 0.2792721 at 100iterations 4.8387786E-03 0.1346474 at 110iterations 2.6434418E-03 9.2487335E-02 at 120iterations finished qdiffx linear iterations at : 12:53:36 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 2.6434418E-03 9.2487335E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 12:53:36 7.054u 0.175s 0:07.49 96.3% 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 Sun Oct 9 2011 at 12:53:36 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 !!! WARNING: GLM 234 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.123172 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): -6.325000 41.82400 ymin,ymax (A): -14.13300 37.16100 zmin,zma (A): 2.031000 44.77400 x,y,z range (A): 48.14900 51.29400 42.74300 scale (grids/A): 3.123172 object centre (A): 17.74950 11.51400 23.40250 number of atom coordinates read : 2405 total number of charged atoms : 2259 net assigned charge : 3.406015 assigned positive charge : 370.0330 centred at (gu) : 91.10361 95.60876 93.41395 assigned negative charge : -366.6274 centred at (gu) : 91.20377 96.34136 94.03835 start vw surface at 0.1500000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 191768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21042 grid for indexing accessible points = 1.400000 m= 101966 mr = 140325 m= 40744 mr = 83782 m= 11453 mr = 33173 m= 2396 mr = 8742 m= 275 mr = 1799 m= 7 mr = 173 m= 0 mr = 0 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 1130 time to turn everything in is 1.840000 number of dielectric boundary points 80615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 18072 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) : 2.082115 object centre at (A) : 17.74950 11.51400 23.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4750457 -2.3230733E-02 midg,1,midg; midg,igrid,midg 0.3924574 -0.5030621 1,midg,midg; igrid,midg,midg 0.7015137 -0.3168215 gauss-seidel spectral radius is 0.9993013 estimated iterations to convergence 298 setup time was (sec) 2.150000 now iterating at: 12:53:39 rms-change max change #iterations 11.10280 466.2847 at 10iterations 6.610924 153.5680 at 20iterations 3.915942 79.47415 at 30iterations 2.320262 40.50009 at 40iterations 1.373931 25.43539 at 50iterations 0.8100551 14.31141 at 60iterations 0.4783266 8.435143 at 70iterations 0.2804683 5.151912 at 80iterations 0.1654482 3.108581 at 90iterations 9.7146057E-02 1.587173 at 100iterations 5.7177018E-02 1.028510 at 110iterations 3.3916987E-02 0.5735283 at 120iterations 2.0296505E-02 0.3880806 at 130iterations 1.2365228E-02 0.2263031 at 140iterations 7.7987444E-03 0.1442165 at 150iterations 5.1842644E-03 0.1101761 at 160iterations 3.6610647E-03 7.5920105E-02 at 170iterations 2.7601221E-03 5.5995941E-02 at 180iterations finished qdiffx linear iterations at : 12:53:48 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 2.7601221E-03 5.5995941E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 12:53:49 11.989u 0.171s 0:12.42 97.8% 0+0k 0+0io 0pf+0w