VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 17 2009 - 13:33:34 CST

Francesco,
  Although I know you've already solved your problem, I thought
I'd give you a tip on the cell measurement question you asked earlier.

In VMD you can use the "measure minmax" command to find the
axis aligned bounding box that contains a given atom selection,
which should give you a rough estimate of your cell dimensions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 17, 2009 at 09:34:23AM +0100, Francesco Pietra wrote:
> In fact, on a rough graphic inspection (with Chimera, I have to learn
> how to do that with VMD) the solvated cell dimensions are
>
> x 147
> y 176
> z 138
>
> My silly mistake is confirmed. Could you please correct the procedure
> I used to measure the cell?
>
> thanks
> francesco
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Thu, Dec 17, 2009 at 9:05 AM
> Subject: Re: Fwd: vmd-l: Re: namd-l: Fwd: conf file for coarse grained
> simulation
> To: Peter Freddolino <petefred_at_ks.uiuc.edu>
>
>
> Hello Peter:
>
> The cell size and center came from:
>
> --launch VMD
>
> --Load solvated .psf and pdb
>
> --Tk Console
>
> --Set all [atomselect top all]
>
> --measure center $all
>   35.1028..  46.859...  28.922...
>
> --measure minmax $all
>  {-39.891...   -43.641...   -40.103...}
>  {109.567...  136.141...   98.125}
>
> (these max values are reasonable for the non-solvated protein+bilayer;
> see at the end my conclusion)
>
> --molinfo top set a 109
>
> --molinfo top set b 136
>
> --molinfo top set c 98
>
> --Graphic repres.. Periodic .. select all x -x y -y z -z
> to get the posted image.
>
> In minimize conf:
> # Periodic Boundary Conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {1} {
> cellBasisVector1    109.    0.   0.
> cellBasisVector2     0.   136.   0.
> cellBasisVector3     0.    0.  98.
> cellOrigin         35.102874755859375 46.8595085144043 28.922983169555664
> }
> wrapWater           on
> wrapAll             on
>
>  #PME (for full-system periodic electrostatics)
> if {1} {
> PME                 yes
> PMEGridSizeX       109
> PMEGridSizeY       136
> PMEGridSizeZ       98
> }
>
> =====
> I did not take
>
>  {-39.891...   -43.641...   -40.103...}
>
> into account when using the Solvate plugin, where:
>
> Boundary 5.0
>
> Use molecule dimensions
>
> Box padding 25 in all six boxes
>
> Use nonstandard solvent
>  cgwat.pdb
>  cgwat.psf
>  rbcg-2007.top
>  side length 40
>  name H2O
> ===
>
> To create the .fix file:
>
> --VMD ... Tk console
>
> --mol load psf ...psf  pdb  ...pdb
>
> --set all [atomselect top "all"]
>
> $all set beta 0
>
> --set fixed [atomselect top "protein or (chain O and name CHO PHO ES1
> ES2 ME1 ME2 ME3 MT1 ME4 ME5 ME6 MT2)"]
>
> $fixed set beta 1
>
> $all writepdb ...fix
>
> whereby POPC got 1.00 in beta column while the cg protein not (how
> should it - and cg water - be named?). I set 1.00 in beta column for
> the protein with a script.
>
> >From your observations it seems to me now -as alluded to above - that
> the method I used to pick up the cell dimensions did not take into
> account the solvation water. If so, it was a most silly overlooking
> because it was clear to me that the protein-bilayer is sized - more or
> less -  109 136 98 A.
>
> thanks
> francesco
>
>
> On Thu, Dec 17, 2009 at 1:49 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> > Hi Francesco,
> > it is pretty apparent from the image that you posted that your periodic
> > cells overlap with each other, meaning lots and lots of clashes are
> > occuring. Have a look at every point where there's an interface between
> > images -- you get double density of water. How did you pick your
> > periodic cell size?
> > Peter
> >
> > Francesco Pietra wrote:
> >> Forgetting about the "steepest descent" procedure, probably
> >> incorrectly devised, I have carefully repeated the procedure in a
> >> water box.
> >>
> >> First I have rebuilt the protein+bilayer model with 4.0A boundary
> >> between the protein and the bilayer (in previous attempts it was
> >> 2.4A). The protein+bilayer could be successfully minimized
> >> non-periodic, no PME, no restraint on any bead:
> >> LINE MINIMIZER BRACKET: DX 9.90228e-07 7.94702e-06 DU -0.00210952
> >> 0.136292 DUDX -4274.13 13.24 34182.2
> >> LINE MINIMIZER REDUCING GRADIENT FROM 54035.7 TO 54.0357
> >> WRITING COORDINATES TO DCD FILE AT STEP 999
> >> TIMING: 1000  CPU: 36.1463, 0.0465229/step  Wall: 81.7678,
> >> 0.0703083/step, 0 hours remaining, 6.966660 MB of memory in use.
> >> PRESSURE: 1000 0 0 0 0 0 0 0 0 0
> >> GPRESSURE: 1000 0 0 0 0 0 0 0 0 0
> >> ETITLE:      TS           BOND          ANGLE          DIHED
> >> IMPRP               ELECT            VDW       BOUNDARY           MISC
> >>        KINETIC               TOTAL           TEMP      POTENTIAL
> >>   TOTAL3        TEMPAVG
> >>
> >> ENERGY:    1000      1266.4280      3301.3107      1238.8463
> >> 0.0000          -5076.5324    -18271.7678         0.0000
> >> 0.0000         0.0000         -17541.7153         0.0000
> >> -17541.7153    -17541.7153         0.0000
> >>
> >> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
> >> WRITING COORDINATES TO DCD FILE AT STEP 1000
> >> WRITING COORDINATES TO RESTART FILE AT STEP 1000
> >> FINISHED WRITING RESTART COORDINATES
> >> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
> >> FINISHED WRITING RESTART VELOCITIES
> >> REINITIALIZING VELOCITIES AT STEP 1000 TO 300 KELVIN.
> >> TCL: Setting parameter numsteps to 10
> >> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10
> >> CLOSING EXTENDED SYSTEM TRAJECTORY FILE
> >> WRITING COORDINATES TO OUTPUT FILE AT STEP 10
> >> CLOSING COORDINATE DCD FILE
> >> WRITING VELOCITIES TO OUTPUT FILE AT STEP 10
> >> ====================================================
> >>
> >> WallClock: 83.922256  CPUTime: 37.538345  Memory: 6.827713 MB
> >> Charmrun> Graceful exit.
> >>
> >> cg Water solvation of the minimized system was then carried out with
> >> Boundary 5.0A and Padding 25A (15+10). In previous attempts it was 4.0
> >> and 19 (15+4).
> >>
> >> Minimization was carried out under the same conditions as in previous
> >> runs (periodic, PME, restraint on the protein and the lipid, which
> >> means that no water was restrained, be that of external solvation or
> >> associated with POPC)
> >>
> >> The simulation halted at step 542 (out of stated 1000) with (as
> >> before) no warning signal. Only one processor was still active 100%
> >> (top monitoring). The simulation started removing clashes (between
> >> solvation waters, or the gap between cell is still not large enough?
> >> please see the attached image of the periodic cells):
> >>
> >> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> >> MINIMIZER SLOWLY MOVING 18573 ATOMS WITH BAD CONTACTS DOWNHILL
> >> PRESSURE: 1 -1.85929e+15 -1.99318e+15 -1.13841e+15 7.73135e+13
> >> 2.58478e+15 -1.60992e+15 2.13888e+14 4.95167e+14 -7.73779e+13
> >> GPRESSURE: 1 -1.85929e+15 -1.99318e+15 -1.13841e+15 7.73135e+13
> >> 2.58478e+15 -1.60992e+15 2.13888e+14 4.95167e+14 -7.73779e+13
> >> ENERGY:       1      1266.4376      3301.3237      1238.8804
> >> 0.0000          -4957.8167 9999999999.9999         0.0000
> >> 0.0000         0.0000      9999999999.9999         0.0000
> >> 9999999999.9999 9999999999.9999         0.0000      9999999999.9999
> >> 9999999999.9999   1452752.0000 9999999999.9999 9999999999.9999
> >>
> >> MINIMIZER SLOWLY MOVING 16749 ATOMS WITH BAD CONTACTS DOWNHILL
> >> OPENING COORDINATE DCD FILE
> >> WRITING COORDINATES TO DCD FILE AT STEP 1
> >> PRESSURE: 2 -9.61887e+13 -9.14159e+13 -5.43871e+13 2.85652e+13
> >> 1.3131e+14 -6.18717e+13 1.15444e+13 2.7896e+13 -6.19013e+12
> >> GPRESSURE: 2 -9.61887e+13 -9.14159e+13 -5.43871e+13 2.85652e+13
> >> 1.3131e+14 -6.18717e+13 1.15444e+13 2.7896e+13 -6.19013e+12
> >> ENERGY:       2      1266.4376      3301.3237      1238.8804
> >> 0.0000          -4957.8167 9999999999.9999         0.0000
> >> 0.0000         0.0000      9999999999.9999         0.0000
> >> 9999999999.9999 9999999999.9999         0.0000      9999999999.9999
> >> 9999999999.9999   1452752.0000 9999999999.9999 9999999999.9999
> >>
> >> and continues so until step 26, than initiates conjugated gradient:
> >>
> >> MINIMIZER SLOWLY MOVING 1 ATOMS WITH BAD CONTACTS DOWNHILL
> >> WRITING COORDINATES TO DCD FILE AT STEP 25
> >> PRESSURE: 26 1.49959e+08 -7.27695e+06 -4.73455e+06 1.66896e+06
> >> 1.50542e+08 -215263 -1.29055e+06 -3.77079e+06 1.51917e+08
> >> GPRESSURE: 26 1.49959e+08 -7.27695e+06 -4.73455e+06 1.66896e+06
> >> 1.50542e+08 -215263 -1.29055e+06 -3.77079e+06 1.51917e+08
> >> ENERGY:      26      1266.4376      3301.3237      1238.8804
> >> 0.0000          -4957.8167 737159432.2607         0.0000
> >> 0.0000         0.0000      737160281.0857         0.0000
> >> 737160281.0857 737160281.0857         0.0000      150806192.8320
> >> 150806192.8320   1452752.0000 150806192.8320 150806192.8320
> >>
> >> MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
> >> LINE MINIMIZER REDUCING GRADIENT FROM 5.31294e+14 TO 5.31294e+11
> >> WRITING COORDINATES TO DCD FILE AT STEP 26
> >> PRESSURE: 27 9.27468e+07 75657.6 -1.68847e+06 1.54594e+06 9.48161e+07
> >> 768612 -1.43932e+06 -1.05566e+06 9.49739e+07
> >> GPRESSURE: 27 9.27468e+07 75657.6 -1.68847e+06 1.54594e+06 9.48161e+07
> >> 768612 -1.43932e+06 -1.05566e+06 9.49739e+07
> >> ENERGY:      27      1266.4376      3301.3237      1238.8804
> >> 0.0000          -4957.8167 463067070.1446         0.0000
> >> 0.0000         0.0000      463067918.9696         0.0000
> >> 463067918.9696 463067918.9696         0.0000       94178916.2476
> >> 94178916.2476   1452752.0000  94178916.2476  94178916.2476
> >>
> >> VDW energy did not improve much, until the procedure halted:
> >>
> >> WRITING COORDINATES TO DCD FILE AT STEP 542
> >> PRESSURE: 543 8.85604e+07 1.45427e+06 -1.39861e+06 1.69754e+06
> >> 9.11258e+07 841076 -1.52223e+06 -717614 9.07388e+07
> >> GPRESSURE: 543 8.85604e+07 1.45427e+06 -1.39861e+06 1.69754e+06
> >> 9.11258e+07 841076 -1.52223e+06 -717614 9.07388e+07
> >> ENERGY:     543      1266.4376      3301.3237      1238.8804
> >> 0.0000          -4957.8167 445412669.1165         0.0000
> >> 0.0000         0.0000      445413517.9415         0.0000
> >> 445413517.9415 445413517.9415         0.0000       90141654.9142
> >> 90141654.9142   1452752.0000  90141654.9142  90141654.9142
> >>
> >>
> >> Well, do you think that the Padding should be increased further, or
> >> that I am doing some silly mistake that has nothing to do with the gap
> >> between cells? I was aware of the Solvate plugin, actually I followed
> >> that. I have reexamined everything without being able to detect were I
> >> am wrong. Do you think worth while trying to restrain the water
> >> associated with POPC?
> >>
> >> Thanks
> >> francesco
> >>
> >>
> >> ---------- Forwarded message ----------
> >> From: Francesco Pietra <chiendarret_at_gmail.com>
> >> Date: Wed, Dec 16, 2009 at 10:01 AM
> >> Subject: Fwd: vmd-l: Re: namd-l: Fwd: conf file for coarse grained simulation
> >> To: Axel Kohlmeyer <akohlmey_at_gmail.com>, Peter Freddolino <petefred_at_ks.uiuc.edu>
> >> Cc: NAMD <namd-l_at_ks.uiuc.edu>
> >>
> >>
> >> Attempts at minimizing under "steepest descent" ended in a crash. I
> >> wonder whether a suggestion may arise from the following.
> >>
> >> Modifications to the conf file:
> >>
> >> set temperature    0
> >>
> >> temperature         $temperature
> >>
> >> langevin            off
> >>
> >> # Minimization
> >> if {1} {
> >> velocityQuenching on
> >> maximumMove 1.5
> >> minimize            1000
> >> reinitvels          $temperature
> >> }
> >>
> >> numsteps 10
> >>
> >> The log said:
> >> .............
> >> Info: Startup phase 7 took 0.0559781 s, 11.754 MB of memory in use
> >> Info: Startup phase 8 took 0.000222921 s, 11.8803 MB of memory in use
> >> Info: Finished startup at 15 s, 11.8803 MB of memory in use
> >>
> >> TCL: Minimizing for 1000 steps
> >> ------------- Processor 2 Exiting: Caught Signal ------------
> >> Signal: segmentation violation
> >> Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
> >> [2] Stack Traceback:
> >>  [0] /lib/libc.so.6 [0x7f4c538daf60]
> >>  [1] _Z24sortEntries_mergeSort_v2RP12__sort_entryS1_i+0xba  [0x5ce526]
> >>  [2] _ZN20ComputeNonbondedUtil32calc_pair_energy_merge_fullelectEP9nonbonded+0x351a
> >>  [0x592c2a]
> >>  [3] _ZN20ComputeNonbondedPair7doForceEPP8CompAtomPP11CompAtomExtPP7Results+0xae4
> >>  [0x57b04e]
> >>  [4] _ZN16ComputePatchPair6doWorkEv+0xa7  [0x6e21a3]
> >>  [5] _ZN11WorkDistrib12enqueueWorkAEP12LocalWorkMsg+0x16  [0x92ed3c]
> >>  [6] _ZN19CkIndex_WorkDistrib31_call_enqueueWorkA_LocalWorkMsgEPvP11WorkDistrib+0xf
> >>  [0x92ed23]
> >>  [7] CkDeliverMessageFree+0x21  [0x9c2d71]
> >>  [8] _Z15_processHandlerPvP11CkCoreState+0x509  [0x9c2365]
> >>  [9] CsdScheduleForever+0xa5  [0xa4bcf5]
> >>  [10] CsdScheduler+0x1c  [0xa4b8f6]
> >>  [11] _Z11master_initiPPc+0x280  [0x508ea0]
> >>  [12] _ZN7BackEnd4initEiPPc+0x31  [0x508c19]
> >>  [13] main+0x2f  [0x5045af]
> >>  [14] __libc_start_main+0xe6  [0x7f4c538c71a6]
> >>  [15] _ZNSt8ios_base4InitD1Ev+0x52  [0x4ff9ea]
> >> Fatal error on PE 2> segmentation violation
> >>
> >>
> >> Thanks
> >> francesco
> >>
> >> ---------- Forwarded message ----------
> >> From: Francesco Pietra <chiendarret_at_gmail.com>
> >> Date: Wed, Dec 16, 2009 at 9:13 AM
> >> Subject: Re: vmd-l: Re: namd-l: Fwd: conf file for coarse grained simulation
> >> To: Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> Cc: NAMD <namd-l_at_ks.uiuc.edu>, Peter Freddolino <petefred_at_ks.uiuc.edu>
> >>
> >>
> >> Thanks a lot for what you wrote. Solvation from scratch with Boundary
> >> 4.0 and Padding 19 (15+4) did not help, or not fully. Minimization at
> >> const. volume (with protein+bilayer restrained) halted at step 532,
> >> out of 1000 set steps.
> >>
> >> The reason to posting now, before I continue to search the right
> >> avenue, is that now the VDW energy has decreased conspicuously, from
> >> initial
> >>
> >> MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
> >> PRESSURE: 3 1.5157e+10 1.03589e+10 4.97618e+09 9.72122e+08 1.2445e+10
> >> -5.9558e+08 -2.86152e+09 -1.00705e+10 1.38611e+09
> >> GPRESSURE: 3 1.5157e+10 1.03589e+10 4.97618e+09 9.72122e+08 1.2445e+10
> >> -5.9558e+08 -2.86152e+09 -1.00705e+10 1.38611e+09
> >> ENERGY:       3      1578.4243      3635.7565      1250.6257
> >> 0.0000          -5656.7864 9999999999.9999         0.0000
> >> 0.0000         0.0000      9999999999.9999         0.0000
> >> 9999999999.9999 9999999999.9999         0.0000      9662690638.0470
> >> 9662690638.0470   1332198.0000 9662690638.0470 9662690638.0470
> >>
> >> MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
> >> PRESSURE: 4 4.34298e+09 6.51726e+09 4.72519e+09 1.90218e+09
> >> 5.44552e+09 3.08174e+09 -2.88084e+07 -4.85553e+08 9.49706e+08
> >> GPRESSURE: 4 4.34298e+09 6.51726e+09 4.72519e+09 1.90218e+09
> >> 5.44552e+09 3.08174e+09 -2.88084e+07 -4.85553e+08 9.49706e+08
> >> ENERGY:       4      1583.3489      3638.1393      1260.5904
> >> 0.0000          -5655.4262 7235356386.7152         0.0000
> >> 0.0000         0.0000      7235357213.3676         0.0000
> >> 7235357213.3676 7235357213.3676         0.0000      3579402107.2727
> >> 3579402107.2727   1332198.0000 3579402107.2727 3579402107.2727
> >>
> >> to final
> >>
> >> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 530
> >> WRITING COORDINATES TO DCD FILE AT STEP 530
> >> WRITING COORDINATES TO RESTART FILE AT STEP 530
> >> FINISHED WRITING RESTART COORDINATES
> >> WRITING VELOCITIES TO RESTART FILE AT STEP 530
> >> FINISHED WRITING RESTART VELOCITIES
> >> PRESSURE: 531 1.53654e+07 3.29332e+06 -372766 543512 1.72077e+07
> >> 1.39373e+06 1.05476e+06 1.19923e+06 1.78077e+07
> >> GPRESSURE: 531 1.53654e+07 3.29332e+06 -372766 543512 1.72077e+07
> >> 1.39373e+06 1.05476e+06 1.19923e+06 1.78077e+07
> >> ENERGY:     531      1600.1030      3648.7438      1294.4447
> >> 0.0000          -5651.9148  73889513.1000         0.0000
> >> 0.0000         0.0000       73890404.4767         0.0000
> >> 73890404.4767  73890404.4767         0.0000       16793614.9574
> >> 16793614.9574   1332198.0000  16793614.9574  16793614.9574
> >>
> >> WRITING COORDINATES TO DCD FILE AT STEP 531
> >> PRESSURE: 532 1.53654e+07 3.29332e+06 -372766 543512 1.72077e+07
> >> 1.39373e+06 1.05476e+06 1.19923e+06 1.78077e+07
> >> GPRESSURE: 532 1.53654e+07 3.29332e+06 -372766 543512 1.72077e+07
> >> 1.39373e+06 1.05476e+06 1.19923e+06 1.78077e+07
> >> ENERGY:     532      1600.1030      3648.7438      1294.4447
> >> 0.0000          -5651.9148  73889513.1000         0.0000
> >> 0.0000         0.0000       73890404.4767         0.0000
> >> 73890404.4767  73890404.4767         0.0000       16793614.9574
> >> 16793614.9574   1332198.0000  16793614.9574  16793614.9574
> >>
> >>
> >> Why the minimizer found it impossible to continue is what I am
> >> wondering about. I am considering:
> >>
> >> ---Before running conjugate gradient, run steepest descent (which is
> >> the rule in Amber). I rely on Peter's 2008 suggestion: "you can get
> >> something very similar by using velocityQuenching (turn on
> >> velocityQuenching and then use run X to run X steps). This method
> >> removes all velocity from all atoms at each step, which gives you a
> >> similar effect. See
> >> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node29.html#8242 for more
> >> details."
> >>
> >> ---Increase Padding or Boundary, or both.
> >>
> >> ---Restrain also the water pertaining to the bilayer, in order to
> >> relax the external solvation water only (may be by setting 1.00 on col
> >> B for POPC water).
> >>
> >> ---Re-building protein+bilayer with a larger boundary (present model
> >> was built with 2.5A boundary between the protein and the bilayer, and
> >> could be minimized with namd under non-periodic conditions. This
> >> notwithstanding,  may be that a larger boundary, 4.0A or so, is
> >> needed).
> >>
> >> That's all i can think about now.
> >>
> >> francesco
> >>
> >> On Tue, Dec 15, 2009 at 6:16 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> >>
> >>> On Tue, 2009-12-15 at 17:01 +0100, Francesco Pietra wrote:
> >>>
> >>>> I forgot to ask: could you please suggest how roughly modify the
> >>>> parameters for cg solvation? I must have misinterpreted the analysis
> >>>> of inter-cell gap. In particular, the relationship between "Boundary"
> >>>> and "Box padding" is not clear to me.
> >>>>
> >>> please have a look at the online help of the solvate command. the
> >>> html file is a bit terse in that respect and should be updated.
> >>> also the URL pointing to the namd tutorial is off by one node...
> >>>
> >>> the boundary value is the distance between the solvent and solute.
> >>> the default value of 2.4 is fairly generous, but due to the increased
> >>> size of water (Martini rolls 4 waters into one site) and protein
> >>> side chain "atoms", stepping this up to, say, 4.0 might be a safe
> >>> choice. this can be easily rationalized from applying common sense:
> >>> just compare the values in an all-atom .par file to the coarse grain
> >>> .par file. the r2min/2 value in the CG .par file is 2.35 whereas the
> >>> corresponding AA values are between 1.3 and 1.8 with a few around 2.0.
> >>>
> >>> since your system was minimizing fine w/o periodicity, the default
> >>> might already be mostly ok for you. these values are empirical anyways.
> >>>
> >>> the padding value is how much solvent outside of min/max dimensions
> >>> of the solute you want to add. so, dimensions of solute _plus_
> >>> padding dimensions will be the new min/max of your system. AFAIK,
> >>> this does not include a "safety" (i.e. the equivalent of boundary for
> >>> inter cell distance), so i would just add that value or more to your
> >>> box dimensions.
> >>>
> >>> when visually checking for overlaps with PBC, you have to increase
> >>> the diameter of your vdw spheres (i just double them for our CMM
> >>> cg model).
> >>>
> >>> HTH,
> >>>   axel.
> >>>
> >>>
> >>>> thanks
> >>>> francesco
> >>>>
> >>>>
> >>> --
> >>> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
> >>> Institute for Computational Molecular Science
> >>> College of Science and Technology
> >>> Temple University, Philadelphia PA, USA.
> >>>
> >>>
> >>>
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078