From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Thu Jul 14 2022 - 12:19:20 CDT

Hi,

Thank you for the response. I can run the CaFE plugin without being in administrator mode now if I change directories prior to starting the program. However, the program is still causing me quite a bit of trouble.

I have created a script to run the CaFE plugin according to the template in the manual:

````
package require cafe 1.0

mmpbsa -top J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/2XQW_Starting_Structure/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/protein.psf \
-trj J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/2XQW_Starting_Structure/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/MD_20stride_protein.dcd \
-out mmpbsa.log \
-debug 2 \
-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_carb.prm \
-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_cgenff.prm \
-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_lipid.prm \
-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_na.prm \
-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/par_all36_prot.prm \
-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/toppar_all36_carb_glycopeptide.str \
-par C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/toppar_water_ions_namd.str \
-com "segname AP1 CP1" \
-rec "segname AP1" \
-lig "segname CP1" \
-first 0 \
-last -1 \
-stride 10 \
-mm 1 \
-pb 1 \
-pb_exe C:/Users/Christos/Downloads/delphicpp_v8.4.4_windows_x64.exe \
-pb_rad mparse \
-sa 1 \
-sa_rad mparse \

quit
````

If I run this script in the VMD TK console with source script_name.vmd, the following prints in the TK console:

````
CaFE) Sanity check
CaFE) Found 5508 atoms for complex
CaFE) Found 4646 atoms for receptor
CaFE) Found 862 atoms for ligand
CaFE) Loaded 10000 frames for complex
CaFE) Generating new trajectory for complex
CaFE) Loaded 10 frames for complex
CaFE) It took 0 days 0 hrs 15 min 52 sec
CaFE) Calculating the MM term
CaFE) It took 0 days 0 hrs 0 min 33 sec
CaFE) Calculating the PB term
Info) ======================
Info) Please cite TopoTools as:
Info) Axel Kohlmeyer & Josh Vermaas, (2019). TopoTools: Release 1.8
Info) https://urldefense.com/v3/__https://doi.org/10.5281/zenodo.598373__;!!DZ3fjg!7HqLy_wRuUwgWsTA93sR348lZhDk93sdXqcdiU9tyg-h3q2ySKrCcnkdFW6-y0YAb1gKgAuKC-QotyYQSNFq3PvlmrHXJnc$
Info) ======================


````
In the VMD console, this is printed:

````
vmd > {C:\Users\Christos\Downloads\CaFE_Plugin-master\CaFE_Plugin-master\cafe1.0} {C:/Program Files/VMD/scripts/tcl8.6} {C:/Program Files/VMD/scripts} {C:/Program Files/lib} {C:/Program Files/VMD/scripts/tk8.6} {C:/Program Files/VMD/scripts/tk8.6/ttk} {C:/Program Files/VMD/scripts/vmd} {C:/Program Files/VMD/plugins/WIN64/tcl} {C:/Program Files/VMD/plugins/noarch/tcl} {C:/Program Files/VMD/plugins/noarch/tcl/tablelist6.11/scripts} c:/Users/Christos/Documents/vmdStore
psfplugin) Detected a Charmm PSF file
Info) Using plugin psf for structure file C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/Morikis_Non_PDBFix_20ns_Test4_QwikMD.psf
Info) Analyzing structure ...
Info) Atoms: 44191
Info) Bonds: 31315
Info) Angles: 22978 Dihedrals: 14830 Impropers: 957 Cross-terms: 348
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 13295
Info) Waters: 12870
Info) Segments: 11
Info) Fragments: 12945 Protein: 2 Nucleic: 0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/2XQW_Starting_Structure/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/MD.dcd
Info) Coordinate I/O rate 10.5 frames/sec, 5 MB/sec, 950.4 sec
Info) Finished with coordinate file J:/pc/Computational_Experiments/Tests/Molecular_Dynamics_Simulations/QwikMD_or_NAMD/2XQW_Starting_Structure/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/MD.dcd.
Info) Opened coordinate file _mmpbsa_com_tmp.dcd for writing.
Info) Finished with coordinate file _mmpbsa_com_tmp.dcd.
psfplugin) Detected a Charmm PSF file
Info) Using plugin psf for structure file C:/Users/Christos/Desktop/Molecular_Dynamics_Setup_Files/CCP19_and_C3d_ChainA_2XQW/Wildtype/Morikis_Non_PDBFix_20ns_Test4/Morikis_Non_PDBFix_20ns_Test4/run/Morikis_Non_PDBFix_20ns_Test4_QwikMD.psf
Info) Analyzing structure ...
Info) Atoms: 44191
Info) Bonds: 31315
Info) Angles: 22978 Dihedrals: 14830 Impropers: 957 Cross-terms: 348
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 13295
Info) Waters: 12870
Info) Segments: 11
Info) Fragments: 12945 Protein: 2 Nucleic: 0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file _mmpbsa_com_tmp.dcd
Info) Finished with coordinate file _mmpbsa_com_tmp.dcd.
Info) Opened coordinate file com_mm_tmp.pdb for writing.
Info) Finished with coordinate file com_mm_tmp.pdb.
Info) Opened coordinate file rec_mm_tmp.pdb for writing.
Info) Finished with coordinate file rec_mm_tmp.pdb.
Info) Opened coordinate file lig_mm_tmp.pdb for writing.
Info) Finished with coordinate file lig_mm_tmp.pdb.
````
Checking the files in the working directory, the only new files created are _mmpbsa_com
_tmp.dcd, com_pb_tmp_0.delphi, com_pb_tmp_0.log, and com_pb_tmp_0.pqr. Since the time is not printed for the PB calculation in the TK console, I believe there is some error in that step. This is what is in the com_pb_tmp_0.log file:

````
 Time> Program started on 2022-7-13 at 18:22:0

   ______________________DelPhi C++ V. 8.4________________________
  | |
  | DelPhi Fortran program was originally developed in Barry Honig|
  | lab to compute electrostatic potential and energies. The |
  | current C++ version is object oriented code, capable of |
  | performing the calculations in sequential, OpenMP and MPI |
  | regimes and the MPI version utilizes distributed memory |
  | technology. Particular novelty is the Gaussian-based smooth |
  | dielectric function that accounts for heterogeneity of the |
  | solute and solute-solvent interface. |
  | |
  | The following reference should be quoted if the use of Delphi |
  | V. 8.0 results to a publication: |
  | |
  | Li, L.; Li, C. A.; Sarkar, S.; Zhang, J.; Witham, S.; |
  | Zhang, Z.; Wang, L.; Smith, N.; Petukh, M.; Alexov, E. |
  | Bmc Biophys 2012, 5. |
  | |
  | For questions and help, visit |
  | https://urldefense.com/v3/__http://compbio.clemson.edu/forum/__;!!DZ3fjg!7HqLy_wRuUwgWsTA93sR348lZhDk93sdXqcdiU9tyg-h3q2ySKrCcnkdFW6-y0YAb1gKgAuKC-QotyYQSNFq3PvlthfLrWU$ |
  | or email to delphi_at_g.clemson.edu |
  | |
  | Jul 2018, by DelPhi Development Team |
  | Chuan Li |
  | Zhe Jia |
  | Arghya Chakravorty |
  | Shailesh K Panday |
  |____________________ ________________________|
                        DelPhi C++ V. 8.4

 Time> Program started on 2022-7-13 at 18:22:0
 No DELPHI keyword, assuming Delphi Format number = 0

 Time> Read in and/or assign rad/chrg done at 2022-7-13 at 18:22:0

 Direct mapping of epsilon : 1/Y
 Grid size : 205
 Percent of box occupied : 80.0000000
 Scale,in grids (1/A) : 2.0000000
 xmin,xmax (A) : -24.4420000 29.3870000
 ymin,ymax (A) : -21.6310000 22.6890000
 zmin,zmax (A) : -32.1830000 41.0060000
 x,y,z range (A) : 53.8290000 44.3200000 73.1890000
 System geometric center (A) : 2.4725000 0.5290000 4.4115000
 Grid box is centered (A) : -0.0000022 0.0000018 0.0000044
 Object centre offset (gu) : 0.0000000 0.0000000 0.0000000
 Outer dielectric : 80.0000000
 Dielectric in Medium 1 : 1.0000000
 First kind salt [C] (M) : 0.0000000
 Valences salt 1 are : 1 1
 Ionic strength (M) : 0.0000000
 Debye length (A) : 1000000.0000000
 Absolute temperature (K) : 297.3342119
 Ion exclusion [r] (A) : 2.0000000
 Probe[r] facing water (A) : 1.4000000
 Probe[r] internal (A) : 1.4000000
 Boundary conditions : COULOMBIC
 # of linear iterations : 1000
 Convergence by rms change : 0.0000000e+000 kT
 Convergence by max change : 1.0000000e-004 kT
 # of non-linear iterations : 0
 Non-linear energy calc. : false
 Manual relaxation para. : false
 GAUSSIAN module : OFF
 Surface potential calculations : OFF

---------- delphicpp finishes IO on 2022-7-13 at 18:22:0

initial cube size too small <<
in assigning accessible points to a grid
therefore rescaling...

---------- delphicpp finishes SPACE class on 2022-7-13 at 18:22:4

 Number of atom coordinates read : 5508
 Total number of assigned charges : 5458
 Net assigned charge : -1.0000000e+000
 Assigned positive charge : 6.6844000e+002
 Centred at (gu) : 1.0308868e+002 1.0265048e+002 1.0298056e+002
 Assigned negative charge : -6.6944000e+002
 Centred at (gu) : 1.0339891e+002 1.0300975e+002 1.0299895e+002
 Number of dielectric boundary points : 48505

 Time> iepsmp to db, and charging done on 2022-7-13 at 18:22:4

 Number of grid points assigned charge : 42944
 Estimated iterations to convergence : 427

 Time> Setup time done on 2022-7-13 at 18:24:9

 Time> Now iterating on 2022-7-13 at 18:24:9

 ----------------------------------------------------------------
       rms-change max change #iterations
 ----------------------------------------------------------------
        1.2937883e+001 6.3730239e+002 at 10 iterations
        8.8709139e+000 3.4293869e+002 at 20 iterations
        6.0674796e+000 2.3828642e+002 at 30 iterations
        4.1639247e+000 1.3604663e+002 at 40 iterations
        2.8395561e+000 9.0397366e+001 at 50 iterations
        1.9446357e+000 6.4476871e+001 at 60 iterations
        1.3297697e+000 4.2012280e+001 at 70 iterations
        9.1122183e-001 3.4131353e+001 at 80 iterations
        6.2125205e-001 1.9523983e+001 at 90 iterations
        4.2627717e-001 1.3991106e+001 at 100 iterations
        2.9137959e-001 9.7747912e+000 at 110 iterations
        1.9899704e-001 6.4038083e+000 at 120 iterations
        1.3591542e-001 4.4289255e+000 at 130 iterations
        9.3565116e-002 3.3180492e+000 at 140 iterations
        6.4048971e-002 2.0771562e+000 at 150 iterations
        4.3709860e-002 1.4723827e+000 at 160 iterations
        2.9954988e-002 9.9881508e-001 at 170 iterations
        2.0562577e-002 6.2912125e-001 at 180 iterations
        1.4075670e-002 4.6693873e-001 at 190 iterations
        9.6600827e-003 3.0084634e-001 at 200 iterations
        6.5924166e-003 2.0925118e-001 at 210 iterations
        4.5222244e-003 1.3845395e-001 at 220 iterations
        3.0912980e-003 9.8435478e-002 at 230 iterations
        2.1167074e-003 6.9366149e-002 at 240 iterations
        1.4494314e-003 4.7023759e-002 at 250 iterations
        9.9422485e-004 3.5413791e-002 at 260 iterations
        6.8225333e-004 2.3576101e-002 at 270 iterations
        4.6532783e-004 1.9656162e-002 at 280 iterations
        3.1972714e-004 1.0458491e-002 at 290 iterations
        2.1978094e-004 7.4923154e-003 at 300 iterations
        1.5038748e-004 4.9500879e-003 at 310 iterations
        1.0302292e-004 3.4639256e-003 at 320 iterations
        7.0623063e-005 2.3622997e-003 at 330 iterations
        4.8460907e-005 1.6322744e-003 at 340 iterations
        3.3367921e-005 1.0916245e-003 at 350 iterations
        2.2998865e-005 7.0422826e-004 at 360 iterations
        1.5766979e-005 5.3364367e-004 at 370 iterations
        1.0849987e-005 3.3850459e-004 at 380 iterations
        7.4916996e-006 2.4519607e-004 at 390 iterations
        5.1819047e-006 1.5956079e-004 at 400 iterations
        3.5959532e-006 1.1743261e-004 at 410 iterations
        2.5045263e-006 7.8172516e-005 at 420 iterations
 ----------------------------------------------------------------
 Info> Iteration ended with final rms-change of 2.5045263e-006
 Info> Run converged in the provided limits

 Time> Finished qdiffx linear iterations 2022-7-13 at 18:24:20
 ----------------------------------------------------------------

---------- delphicpp finishes SOLVER class on 2022-7-13 at 18:24:20

 Energy> Total grid energy : 318675.55 kT
 Energy> Corrected reaction field energy : -8422.30 kT
 Energy> All required energy terms but grid energy : -8422.30 kT

---------- delphicpp finishes ENERGY class on 2022-7-13 at 18:24:21

---------- delphicpp finishes SITE class on 2022-7-13 at 18:24:21

 Time> Total CPU time is 0:2:20

 Time> Delphi exited on 2022-7-13 at 18:24:21

 ......... PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 1 WARNING(S) ........

 ..................... SHOWING 1 OUT OF 1 WARNING(S) ...................
   
[WARNING #1] IN PARAMETER FILE, USER SPECIFIES TO READ PDB FILE IN MODIFIED FORMAT (CHARGE AND SIZE ARE READ FROM THE PDB FILE AS WELL)

````

Can you please provide any insight into this warning/error? I believe it is causing the rest of the CaFE program to not run, so the final mmpbsa.log file is not generated. I am not sure how there can be a warning or error regarding a PDB file when I only provide a psf and dcd file to the CaFE program. Please let me know if I can provide any additional information to help solve this problem.

Thank you so much for your help.

Best,
Christos
________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Wednesday, July 6, 2022 7:29 AM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
Cc: Jason Smith <jason_smith_18_at_sfu.ca>; Ashar Malik <asharjm_at_gmail.com>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Error with CaFE VMD Plugin

⚠ Caution: External sender

Hi,
  It shouldn't be necessary to run VMD as Administrator if file permissions
and your working directory are set appropriate when you're using plugins
that write output files in intermediate steps for launching NAMD or similar
apps. You should be able to check what environment variables you have set
in Windows (globally) that impact VMD. Both the 32-bit and 64-bit versions
pay attention to environment variables, so off the top of my head I don't
have an answer for why you'd get different behavior with respect to finding
NAMD automatically unless you have different path environment variables in
the two cases.

Best,
  John Stone

On Fri, Jun 17, 2022 at 11:22:28AM +0000, Efthymiou, Christos wrote:
> Thank you for the advice! Running VMD in administrator mode seems to fix
> the previous problem, but now I am having trouble with VMD recognizing
> namd. I get the following error:
> ````
> (VMD) 12 % source CaFE_Script.vmd
> CaFE) Sanity check
> CaFE) Found 5508 atoms for complex
> CaFE) Found 4646 atoms for receptor
> CaFE) Found 862 atoms for ligand
> CaFE) Loaded 8411 frames for complex
> CaFE) Generating new trajectory for complex
> CaFE) Loaded 9 frames for complex
> CaFE) It took 0 days 0 hrs 12 min 37 sec
> CaFE) Calculating the MM term
> couldn't execute "namd2": no such file or directory
> ````
> I just recently downloaded the 64bit version of VMD which is what I am
> using for this plugin, but I originally downloaded the 32bit VMD 1.9.3 and
> NAMD together, and that still seems to work. How do I make the latest
> version of VMD recognize that namd is on my computer? I can't recall how I
> made it work previously for the 32bit version of VMD.
> Thank you again for all the help.
>
> --------------------------------------------------------------------------
>
> From: Jason Smith <jason_smith_18_at_sfu.ca>
> Sent: Thursday, June 16, 2022 4:50 PM
> To: Ashar Malik <asharjm_at_gmail.com>; Efthymiou, Christos
> <christos.dereschuk.20_at_ucl.ac.uk>
> Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: Error with CaFE VMD Plugin
>
>
> ** Caution: External sender
>
> My Experience with VMD in general (not having used CaFE specifically) is
> that this is indeed a common problem on windows not having file
> permissions in the default c:\whatever locations. With science programs in
> general, I be sure to look for things like all read/write operations
> occurring in a location I have all permissions for, running in
> administrator mode if necessary/possible, and checking whether the program
> is attempting to run in UAC mode.
>
> Cheers,
>
> -
> Jason Smith
> Post-Doctoral Fellow
> Robert N. Young Lab, Simon Fraser University
> 8888 University Drive, Burnaby, BC, V5A-1S6
> Canada
>
> --------------------------------------------------------------------------
>
> From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ashar
> Malik <asharjm_at_gmail.com>
> Sent: Thursday, 16 June 2022 4:32:12 AM
> To: Efthymiou, Christos
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Error with CaFE VMD Plugin
>
> My experience with this kind of error (for general work not related to
> CaFE) was in 2014 when we had VMD running on Windows machines in the
> labs.
> This was overcome by running vmd in administrator mode or changing the
> working path to a location where you have read/write access.
> Hope this helps.
> On Thu, Jun 16, 2022 at 7:13 PM Efthymiou, Christos
> <[1]christos.dereschuk.20_at_ucl.ac.uk> wrote:
>
> Hello,
> I have run some molecular dynamics simulations on a protein-protein
> complex and I would like to use the CaFE VMD plugin to calculate the
> free binding energy of this association. I am using a Windows 10
> computer and have both the 32bit and 64bit versions of VMD available. I
> downloaded the code from github
> here [2]https://urldefense.com/v3/__https://github.com/HuiLiuCode/CaFE_Plugin__;!!DZ3fjg!7HqLy_wRuUwgWsTA93sR348lZhDk93sdXqcdiU9tyg-h3q2ySKrCcnkdFW6-y0YAb1gKgAuKC-QotyYQSNFq3PvlfZlPc3o$ and followed the
> manual to set everything up for the program to work within VMD.
> The first problem I experience is when I try to run the program
> according to the command given in the manual. To run the program, the
> manual says to use the command
> vmd -dispdev text -eofexit < script.vmd > vmd.log
> When I try to run that command, I get the following error:
> couldn't write file "vmd.log": permission denied
> In any case, when I instead use the standard command of source
> script.vmd, the program runs and prints the following:
> CaFE) Sanity check
> CaFE) Found 5508 atoms for complex
> CaFE) Found 4646 atoms for receptor
> CaFE) Found 862 atoms for ligand
> CaFE) Loaded 10000 frames for complex
> CaFE) Generating new trajectory for complex
> Unable to load file '_mmpbsa_com_tmp.dcd' using file type 'dcd'.
> I am not sure what the _mmpbsa*_com_tmp.dcd file is, or why the program
> is unable to open it. Please let me know if you have any solution to
> this problem as I really would like to be able to use this program for
> calculating free binding energy.
>
> References
>
> Visible links
> 1. mailto:christos.dereschuk.20_at_ucl.ac.uk
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Research Affiliate, NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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