2016-03-26 BLFoley This file contains information regarding the contents of the directory in which it residues. This directory contains files relevant to a paper recently submitted to JACS. Paper info: * Submitted to JACS on 18 March, 2016, Manuscript ID: ja-2016-02879s * Title: The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate * Authors (current approximate list & order): Che-Hsiung Hsu, Sangho Park, David E. Mortenson, B. Lachele Foley, Xiaocong Wang, Robert J. Woods, David, A. Case, Evan T. Powers, Chi-Huey Wong, H. Jane Dyson, Jeffery W. Kelly Additional info can be found here: http://128.192.9.183/eln/lachele/2016/03/25/generation-of-lidop-structures-for-hsu-et-al-carb-aromatic-interaction-strengths/ At some point in the near future, the above link will probably change to: http://woods.ccrc.uga.edu/lachele/2016/03/25/generation-of-lidop-structures-for-hsu-et-al-carb-aromatic-interaction-strengths/ The following is a tree-style listing of the archive contents, with notes . ├── 00_README This file ├── initial_coordinates Directory containing files relevant to the initial coordinates used during the simulations referenced in the paper │   ├── 2M9E.pdb Initial PDB file for the protein │   ├── allose_2m9f.pdb -- pdb glycosylated with allose │   ├── allose_prmtop -- parm/top file for allose-glycosylated version │   ├── Galactose_2m9f.pdb -- ... pdb with galactose │   ├── galactose_prmtop -- ... parm/top with galactose │   ├── Lidose_2m9f.pdb -- ... with idose │   ├── lidose_prmtop -- ... │   ├── xylose_2m9f.pdb -- ... with xylose │   └── xylose_prmtop -- ... │   ├── leaprc.ff99SBildn.nmr Custom parameter file used for the protein │   ├── leap_Lidose_1C4.in Sample leap input for glycosylation with alpha idose │   ├── Lidose_1C4.parm7 -- parm/top file for alpha-idose glycosylated version │   ├── Lidose_1C4.pdb -- corresponding PDB-style file │   ├── Lidose_1C4.rst7 -- corresponding input/coordinate file │   ├── leap_Lidose_1C4b.in Sample leap input for glycosylation with beta idose │   ├── Lidose_1C4b.parm7 -- Same as lidose_prmtop │   ├── Lidose_1C4b.pdb -- corresponding PDB-style file │   ├── Lidose_1C4b.rst7 -- corresponding input/coordinate file │   ├── min1_1C4.pdb Quickly-minimized alpha-idose glycosylated version for sanity check │   ├── min1_1C4b.pdb -- ... the beta-idose version │   ├── orient.nab NAB input file used for aligning the idose to the protein's coords ├── MD_coordinates Directory containing trajectory snapshots from the simulations. Each zipped archive contains 100 snapshots. For analysis, pair with the parm/top file noted │   ├── allose.zip -- pair with allose_prmtop │   ├── galactose.zip -- ... with galactose_prmtop │   ├── lidose.zip -- ... with lidose_prmtop │   └── xylose.zip -- ... with xylose_prmtop ├── MD_method_info Directory containing information related to the methods used in the simulations. │   ├── anneal1gbf.xylose.tmp Sample mdin for the production (annealing) run │   ├── method.docx Procedural overview │   ├── minmizgb.xylose.tmp Sample mdin file for the minimization of the complex │   ├── m.xylose.001.o Sample mdout file that contains full details of the run conditions │   ├── protongb.xylose.tmp Sample mdin for the minimization of the protons │   └── run.txt Sample run submission script └── Prep_file_development_details Directory containing files relevant to the generation of the prep files. 1. Sets of files for alpha/beta and 4C1/1C4: All four file sets follow the pattern specified in the first set. ├── 0IA_4C1_58.pdb The D-analog coordinate file ├── D_0IA_4C1_noROH_charges.txt The D-analog charge set ├── 0IA_1C4_58_L.pdb The L-analog made by inverting the x-axis coordinates ├── 0IA_1C4_58_L_noROH.pdb The L-analog PDB file minus the ROH residue atoms ├── 0IA_1C4_58_L_noROH.prep Interim prep file with incorrect atom type names ├── 0IA_1C4_L.prep Final L-analog prep file with correct atom type names ├── leap_0IA_1C4_L Leap input file for testing the prep file ├── 0IA_1C4_L.parm7 -- parm/top from the test ├── 0IA_1C4_L.rst7 -- inp/crd from the test ├── 0IA_1C4_71.pdb Follows pattern of first group ├── D_0IA_1C4_noROH_charges.txt ├── 0IA_4C1_71_L.pdb ├── 0IA_4C1_71_L_noROH.pdb ├── 0IA_4C1_71_L_noROH.prep ├── 0IA_4C1_L.prep ├── leap_0IA_4C1_L ├── 0IA_4C1_L.parm7 ├── 0IA_4C1_L.rst7 ├── 0IB_4C1_60.pdb Follows pattern of first group ├── D_0IB_1C4_noROH_charges.txt ├── 0IB_1C4_60_L.pdb ├── 0IB_1C4_60_L_noROH.pdb ├── 0IB_1C4_60_L_noROH.prep ├── 0IB_1C4_L.prep ├── leap_0IB_1C4_L ├── 0IB_1C4_L.parm7 ├── 0IB_1C4_L.rst7 ├── 0IB_1C4_77.pdb Follows pattern of first group ├── D_0IB_4C1_noROH_charges.txt ├── 0IB_4C1_77_L.pdb ├── 0IB_4C1_77_L_noROH.pdb ├── 0IB_4C1_77_L_noROH.prep ├── 0IB_4C1_L.prep ├── leap_0IB_4C1_L ├── 0IB_4C1_L.parm7 ├── 0IB_4C1_L.rst7 2. Sets of files relevant to all prep files ├── Lowest_Energy_frames.txt List of the lowest energy frames (see QM_info, below) ├── how-to-make-the-preps.txt Brief overview of prep-file-making procedure ├── run_Chairs.sh BASH script used to generate the prep files ├── MAIN_CHAIN.txt Main chain info file used in run_Chairs.sh 3. Files used in choosing initial coordinates ├── QM_info Information used in determining the lowest-QM-energy coordinates │   ├── A_1C4 │   │   ├── scf_energies_sorted.txt The file scf_energies.txt, sorted by energy │   │   └── scf_energies.txt Energies as extracted from the G09 QM log files │   ├── A_4C1 │   │   ├── scf_energies_sorted.txt │   │   └── scf_energies.txt │   ├── B_1C4 │   │   ├── scf_energies_sorted.txt │   │   └── scf_energies.txt │   └── B_4C1 │   ├── scf_energies_sorted.txt │   └── scf_energies.txt 4. File archive sent to Hsu, et al. ├── LIdo_to_send_2015-11-04 │   ├── 0IA_1C4_58_L.pdb -> ../0IA_1C4_58_L.pdb │   ├── 0IA_1C4_L.prep -> ../0IA_1C4_L.prep │   ├── 0IA_4C1_71_L.pdb -> ../0IA_4C1_71_L.pdb │   ├── 0IA_4C1_L.prep -> ../0IA_4C1_L.prep │   ├── 0IA_OS2_78_L.pdb -> ../0IA_OS2_78_L.pdb │   ├── 0IB_1C4_60_L.pdb -> ../0IB_1C4_60_L.pdb │   ├── 0IB_1C4_L.prep -> ../0IB_1C4_L.prep │   ├── 0IB_4C1_77_L.pdb -> ../0IB_4C1_77_L.pdb │   ├── 0IB_4C1_L.prep -> ../0IB_4C1_L.prep │   ├── 0IB_OS2_75_L.pdb -> ../0IB_OS2_75_L.pdb │   ├── 0IB_OS2_L.prep -> ../0IB_OS2_L.prep │   ├── leap_0IA_1C4_L -> ../leap_0IA_1C4_L │   ├── leap_0IA_4C1_L -> ../leap_0IA_4C1_L │   ├── leap_0IB_1C4_L -> ../leap_0IB_1C4_L │   ├── leap_0IB_4C1_L -> ../leap_0IB_4C1_L │   └── Show_LIdopa_in_1C4.jpg 5. Aligned structure files from David Case ├── from_DAC │   ├── leapin │   ├── leap_LIdo_1C4_A_BLF.in │   ├── leap_Lidose_1C4b.in │   ├── leap_Lidose_1C4.in │   ├── leap.log │   ├── Lidose_1C4b.parm7 │   ├── Lidose_1C4b.rst7 │   ├── Lidose_1C4.parm7 │   ├── Lidose_1C4.pdb │   ├── Lidose_1C4.rst7 │   ├── orient.nab │   └── x.pdb 6. Files used to produce images for communicating with other authors └── Visualization ├── Show_0IA_1C4_L.vmd ├── Show_LIdopa_in_1C4 ├── Show_LIdopa_in_1C4_cropped.png ├── Show_LIdopa_in_1C4.jpg └── Show_LIdopa_in_1C4.tga The files below this were not used in the study but are included for historical accuracy ├── 0iAa_1C4.prep Early versions of prep files sent to Oliver C. Grant ├── 0iAb_4C1.prep ├── 0iBa_1C4.prep ├── 0iBb_4C1.prep ├── to_oliver The file archive sent to Oliver │   ├── 0iAa_1C4_58_noROH.pdb │   ├── 0iAa_1C4_58.pdb │   ├── 0iAa_1C4.prep │   ├── 0iAb_4C1_71_noROH.pdb │   ├── 0iAb_4C1_71.pdb │   ├── 0iAb_4C1.prep │   ├── 0iBa_1C4_60_noROH.pdb │   ├── 0iBa_1C4_60.pdb │   ├── 0iBa_1C4.prep │   ├── 0iBb_4C1_77_noROH.pdb │   ├── 0iBb_4C1_77.pdb │   ├── 0iBb_4C1.prep │   ├── protein_with_rough_ido_from_DAC.pdb │   └── README ├── from_oliver File archive later returned from Oliver Oliver's files are certainly fine, but the problem was solved before he got them back to us, so they weren't used. │   ├── protein_0iAa_1C4_58_aligned.pdb │   ├── protein_0iAb_4C1_71_aligned.pdb │   ├── protein_0iBa_1C4_60_aligned.pdb │   ├── protein_0iBb_4C1_77_aligned.pdb │   └── rebuildgp.zip ├── 2SO_OS2 Files for the 2SO and OS2 ring structures. The set of files is incomplete because these conformers were not needed. │   ├── 0IA_2SO_78.pdb │   ├── 0IA_OS2_78_L.pdb │   ├── 0IB_2SO_75.pdb │   ├── 0IB_2SO_charges.txt │   ├── 0IB_OS2_75_L_noROH.pdb │   ├── 0IB_OS2_75_L_noROH.prep │   ├── 0IB_OS2_75_L.pdb │   ├── 0IB_OS2_L.prep │   ├── 0IB_OS2_noROH_charges.txt │   ├── A_2SO │   │   ├── scf_energies_sorted.txt │   │   └── scf_energies.txt │   └── B_2SO │   ├── scf_energies_sorted.txt │   └── scf_energies.txt