Tue Oct 11 08:18:38 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 Tue Oct 11 2011 at 08:18:39 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 0.6606785 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): -24.80500 21.83100 ymin,ymax (A): -64.38800 -10.50400 zmin,zma (A): -17.22900 30.30300 x,y,z range (A): 46.63600 53.88400 47.53200 scale (grids/A): 0.6606785 object centre (A): -1.487000 -37.44600 6.537000 number of atom coordinates read : 2700 total number of charged atoms : 2565 net assigned charge : 4.000021 assigned positive charge : 414.7145 centred at (gu) : 90.64123 89.89648 90.47047 assigned negative charge : -410.7154 centred at (gu) : 90.47846 90.13403 90.49652 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8001 nv = 96 ne = 84 npr = 55322 no. pairs analyzed = 55322 no. exposed pairs = 3301 no. arc points = 22501 no. surface atoms = 1118 nbur = 1582 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 4647 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2159 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4271043E-08 5.0280264E-09 midg,1,midg; midg,igrid,midg 6.0842851E-08 -4.0820801E-08 1,midg,midg; igrid,midg,midg -2.1859421E-08 5.0647905E-08 gauss-seidel spectral radius is 0.9881341 estimated iterations to convergence 75 setup time was (sec) 0.5900000 now iterating at: 08:18:39 rms-change max change #iterations 0.1780015 22.81762 at 10iterations 1.9601217E-02 2.791840 at 20iterations 3.1930064E-03 0.5807877 at 30iterations 1.0361354E-03 0.2042542 at 40iterations 4.1017655E-04 8.0970764E-02 at 50iterations finished qdiffx linear iterations at : 08:18:44 total time elapsed so far: 4.660000 # loops : 50 mean,max change (kT/e) : 4.1017655E-04 8.0970764E-02 energy calculations done at 4.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.820000 DelPhi exited at 08:18:44 4.822u 0.380s 0:05.65 92.0% 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 Tue Oct 11 2011 at 08:18:44 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 1.982036 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): -24.80500 21.83100 ymin,ymax (A): -64.38800 -10.50400 zmin,zma (A): -17.22900 30.30300 x,y,z range (A): 46.63600 53.88400 47.53200 scale (grids/A): 1.982036 object centre (A): -1.487000 -37.44600 6.537000 number of atom coordinates read : 2700 total number of charged atoms : 2565 net assigned charge : 4.000021 assigned positive charge : 414.7145 centred at (gu) : 91.92326 89.68869 91.41059 assigned negative charge : -410.7154 centred at (gu) : 91.43502 90.40195 91.48937 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86085 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22501 grid for indexing accessible points = 1.400000 m= 33004 mr = 61338 m= 5754 mr = 25039 m= 423 mr = 3791 m= 8 mr = 188 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 285 time to turn everything in is 0.7100000 number of dielectric boundary points 34919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 20253 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) : 0.6606785 object centre at (A) : -1.487000 -37.44600 6.537000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4593610E-02 -2.4139484E-02 midg,1,midg; midg,igrid,midg 7.2599530E-02 -4.7871307E-02 1,midg,midg; igrid,midg,midg -1.5875999E-02 5.0753634E-02 gauss-seidel spectral radius is 0.9987471 estimated iterations to convergence 224 setup time was (sec) 1.030000 now iterating at: 08:18:58 rms-change max change #iterations 4.767676 193.0340 at 10iterations 2.302265 73.66681 at 20iterations 1.112389 30.48833 at 30iterations 0.5363799 15.45269 at 40iterations 0.2615462 8.917517 at 50iterations 0.1262902 3.678001 at 60iterations 6.1463468E-02 1.815838 at 70iterations 3.0016711E-02 0.8336411 at 80iterations 1.4927239E-02 0.4627142 at 90iterations 7.6039340E-03 0.2456131 at 100iterations 4.0896651E-03 0.1432419 at 110iterations 2.3862720E-03 9.3528748E-02 at 120iterations finished qdiffx linear iterations at : 08:19:09 total time elapsed so far: 11.86000 # loops : 120 mean,max change (kT/e) : 2.3862720E-03 9.3528748E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 08:19:10 12.030u 0.469s 0:25.36 49.2% 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 Tue Oct 11 2011 at 08:19:10 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 2.973053 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): -24.80500 21.83100 ymin,ymax (A): -64.38800 -10.50400 zmin,zma (A): -17.22900 30.30300 x,y,z range (A): 46.63600 53.88400 47.53200 scale (grids/A): 2.973053 object centre (A): -1.487000 -37.44600 6.537000 number of atom coordinates read : 2700 total number of charged atoms : 2565 net assigned charge : 4.000021 assigned positive charge : 414.7145 centred at (gu) : 92.88485 89.53293 92.11577 assigned negative charge : -410.7154 centred at (gu) : 92.15237 90.60285 92.23412 start vw surface at 0.1200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 199070 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22501 grid for indexing accessible points = 1.400000 m= 105486 mr = 147956 m= 40539 mr = 87983 m= 10492 mr = 33276 m= 1820 mr = 8096 m= 131 mr = 1309 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 988 time to turn everything in is 1.870000 number of dielectric boundary points 78877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 20513 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) : 1.982036 object centre at (A) : -1.487000 -37.44600 6.537000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2097025 -0.2875752 midg,1,midg; midg,igrid,midg 0.9796659 -0.6303467 1,midg,midg; igrid,midg,midg -0.1735307 0.4076724 gauss-seidel spectral radius is 0.9992862 estimated iterations to convergence 295 setup time was (sec) 2.220000 now iterating at: 08:19:12 rms-change max change #iterations 10.97611 357.4930 at 10iterations 6.462573 143.1770 at 20iterations 3.802674 82.00947 at 30iterations 2.225518 52.60415 at 40iterations 1.303927 23.29368 at 50iterations 0.7610251 12.99551 at 60iterations 0.4439505 8.018391 at 70iterations 0.2592236 4.339427 at 80iterations 0.1512460 2.633618 at 90iterations 8.8093087E-02 1.714616 at 100iterations 5.1340334E-02 0.9133720 at 110iterations 3.0024158E-02 0.5465736 at 120iterations 1.7679293E-02 0.3097649 at 130iterations 1.0460600E-02 0.1948318 at 140iterations 6.3587199E-03 0.1256866 at 150iterations 3.9864536E-03 9.3444824E-02 at 160iterations 2.6556351E-03 5.7975769E-02 at 170iterations 1.8948455E-03 4.5495033E-02 at 180iterations finished qdiffx linear iterations at : 08:19:30 total time elapsed so far: 19.55000 # loops : 180 mean,max change (kT/e) : 1.8948455E-03 4.5495033E-02 energy calculations done at 19.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.72000 DelPhi exited at 08:19:30 19.729u 0.455s 0:20.66 97.6% 0+0k 0+0io 0pf+0w