File: Parm_Docs/Glycam_06.txt =================================== The following valence bond/angle parameters were replaced in the first peer-review submitted version of GLYCAM06 (Glycam_06.dat_FirstSubmission_JCC) with those from AMBER's Parm94/Parm99 parameter files From: C -OS 409.0 1.33 To: C -OS 450.0 1.323 Parm99 From: CG-HC 360.0 1.095 Ethane CG-H1 410.0 1.092 Methanol CG-H2 440.0 1.105 1,1-Dimethoxyethane To: CG-HC 340.0 1.090 Parm94 CG-H1 340.0 1.090 Parm94 CG-H2 340.0 1.090 Parm94 From: C -O 999.0 1.220 N-Methylethanamide C -N 490.0 1.360 N-Methylethanamide C -O2 730.0 1.260 2-Methylpropanoate To: C -O 570.0 1.229 Parm94 C -N 490.0 1.335 Parm94 C -O2 656.0 1.250 Parm94 From: OH-HO 700.0 0.960 Methanol To: OH-HO 553.0 0.960 Parm94 From: N -H 600.0 1.010 N-Methylethanamide To: N -H 434.0 1.010 Parm94 From: OS-C -O 132.0 122.20 K calculated from methyl acetate (eqm value from crystal average) To OS-C -O 80.0 125.00 Parm99 From: O2-C -O2 100.00 130.00 Acetate, 2-Methylpropanoate To: O2-C -O2 80.00 126.00 Parm94 From: N -C -O 80.00 122.70 Force constant taken from Parm94, Angle set to HF/6-31G(d) value N-Methylethanamide To: N -C -O 80.00 122.90 Parm94 From: C -N -H 60.00 122.00 Ethanamide H -N -H 30.00 119.00 Force constant taken from Parm94, Angle set to agree with C -N -H in ethanamide To: C -N -H 30.00 122.00 Parm94 H -N -H 35.00 120.00 Parm94 From: H1-CG-N 35.00 109.50 Parm91 H-CG-N H2-CG-N 35.00 109.50 Parm91 H-CG-N To: H1-CG-N 50.00 109.50 Parm94 H1-CT-N H2-CG-N 50.00 109.50 Parm94 H1-CT-N File: Parm_Docs/Glycam_06g.txt =================================== #### Change log for 2011-09-15 #### Changed by BLFoley to create Glycam_06g-1.dat Corrected typo in torsion: -NH-CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages +N -CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages #### Change log for 2011-07-06 #### #### BLFoley #### Adding an approximate date for the public release of Glycam_06g.dat. (actual date lost) Estimated date: 8 July, 2010 # Glycam_06g.dat # Changes include adding a comprehensive thiol-linkage set for glycosidic linkages formed by a Sulfur # as well as N-Sulfate terms, updated ring-torsions, and sialic acid torsions # New 1,4-scaling setup has been added to the torsions section ### ## Changed the following terms from: # Angles OS-P -OS 45.0 102.6 Parm94 P -OS-CP 50.0 121.0 K calculated from dimethyl phosphate (eqm value from crystal average) # Torsions OS-CG-CG-OS 1 0.82 0.0 2. DiEthers OS-CG-CP-OS 1 0.82 0.0 2. Copy of OS-CG-CG-OS CG-CG-OS-C 1 -0.04 0.0 -3 Ethyl acetate, 2-Methoxy 3-O-Acetyl THP 1 0.47 0.0 1 CG-OS-C -O 1 -3.20 0.0 2 Methyl acetate CG-C -OS-CG 1 -3.0 0.0 2 Methyl acetate - CORRECTED CG-OS-CY-C 1 3.50 0.0 1. 1-Methoxy-1-Acetate THP, 1-Methoxy-1-Acetate THP Acid w/ Hbond - for sialic acid only! ## to: # Angles OS-P -OS 45.0 109.6 Parm94 and changed eqm value for better reproduction of average of crystal structures P -OS-CP 50.0 119.0 K calculated from dimethyl phosphate (eqm value from crystal average) C -N -H 60.00 122.00 Ethanamide # Torsions OS-CG-CP-OS 1 0.40 0.0 2. !G06g - Copy of OS-CG-CG-OS, original 0.82 OS-CG-CG-OS 1 0.40 0.0 2. !G06g - DiEthers, original 0.82 CG-CG-OS-C 1 -0.01 0.0 -3 Ethyl acetate, 2-Methoxy 3-O-Acetyl THP 1 0.04 0.0 -2 1 0.12 0.0 1 CG-OS-C -O 1 0.0 0.0 -3 Cyclohexyl acetate (axial and equatorial) 1 -2.90 0.0 -2 1 0.60 0.0 1 CG-C -OS-CG 1 0.0 0.0 -3 Cyclohexyl acetate (axial and equatorial) 1 -2.90 0.0 -2 1 -0.60 0.0 1 CG-OS-CY-C 1 1.90 0.0 1. 1-Methoxy-1-Acetate THP, 1-Methoxy-1-Acetate THP Acid w/ Hbond - for sialic acid only! # but did not change: OS-CG-CG-OY 1 0.82 0.0 2. DiEthers - sialic acid only #### # Added the following terms: # Bonds S -N 238.0 1.675 N-Sulfate - Using avg value from ZULPIF and ZULPIF01 (CSD 1.638 A) # Angles H2-CG-SM 41.5 109.6 Avg value from set of CSD crystal structures 109.2 deg OS-CG-SM 68.0 108.3 Avg value from set of CSD crystal structures 108.3 deg S -N -CG 31.0 110.0 avg value from ZULPIF & ZULPIF01 118.4 deg O2-S -N 84.0 108.0 avg value from ZULPIF & ZULPIF01 106.4 deg S -N -H 37.5 121.2 avg value from QM 6-31++g** 114.0 deg (ethylsulfamate) CP-OS-CG 50.00 111.60 Copy of CG-OS-CG CP-CG-N 80.00 109.70 Copy of CG-CG-N # Torsions O2-S -N -H 1 -0.10 0.0 6. N-Sulfates O2-S -N -CG 1 0.11 0.0 -3. N-Sulfates 1 0.00 0.0 -2. 1 0.00 0.0 1. S -N -CG-H1 1 0.02 0.0 3. N-Sulfates S -N -CG-CG 1 0.00 0.0 -3. N-Sulfates 1 -1.25 0.0 -2. 1 -4.00 0.0 1. CG-OS-CG-SM 1 0.67 0.0 -3. Thiol-linkages 1 1.90 0.0 -2. 1 1.14 0.0 1. OS-CG-SM-CG 1 1.03 0.0 -3. (methoxymethyl)(methyl)sulfane 1 1.44 0.0 -2. 1 0.27 0.0 1. H2-CG-SM-CG 1 0.0 0.0 1. (methoxymethyl)(methyl)sulfane SM-CG-CG-H2 1 0.28 0.0 -3. (2,2-dimethoxyethyl)(methyl)sulfane 1 0.04 0.0 -2. 1 -0.21 0.0 1. SM-CG-CG-OS 1 0.03 0.0 -3. (2-methoxyethyl)(methyl)sulfane 1 0.18 0.0 -2. 1 -1.03 0.0 1. File: Parm_Docs/Glycam_06f.txt =================================== #### Change log for 2011-09-15 #### Changed by BLFoley to create Glycam_06f-1.dat Corrected typo in torsion: -NH-CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages +N -CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages #### Change log for 2009-02-03 #### -- Corrected sign typo for O-Acetyl group CG-C -OS-CG #Changed from CG-C -OS-CG 1 3.0 0.0 2 Methyl acetate #Changed to CG-C -OS-CG 1 -3.0 0.0 2 Methyl acetate File: Parm_Docs/Glycam_06e.txt =================================== #### Change log for 2011-09-15 #### Changed by BLFoley to create Glycam_06e-1.dat Corrected typo in torsion: -NH-CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages +N -CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages #### Change log for 2008-05-20 #### -- updated torsion parameters for endo/exocyclic terms CG-OS-CG-OS CG-OS-CG-C OS-CP-OS-CG CG-OS-CG-C CG-CG-C -O2 OS-CG-C -O2 OS-CG-OS-CG 1 0.96 0.0 -3. 2,2-Dimethoxypropane 1 1.38 0.0 -2. 1 1.08 0.0 1. OS-CP-OS-CG 1 0.96 0.0 -3. Copy of OS-CG-OS-CG (not derived) 1 1.38 0.0 -2. 1 1.08 0.0 1. OH-CG-OS-CG 1 0.96 0.0 -3. Copy of OS-CG-OS-CG (not derived) 1 1.38 0.0 -2. 1 1.08 0.0 1. CG-OS-CG-C 1 0.32 0.0 -3. 1-Methoxy-1-Acetate THP, 1-Methoxy-1-Acetate THP Neutralized w/ Hbond 1 0.45 0.0 -2. 1 -0.60 0.0 1. CG-CG-C -O2 2 0.02 0.0 -3. Propanoate, 2-Methylpropanoate, 2-Dimethylpropanoate 2 -0.82 0.0 -2. 2 0.01 0.0 1. OS-CG-C -O2 2 0.04 0.0 -3. 2-Methoxy-2-methylpropanoate 2 -1.45 0.0 -2. 2 0.04 0.0 1. File: Parm_Docs/Glycam_06d.txt =================================== #### Change log for 2011-09-15 #### Changed by BLFoley to create Glycam_06d-1.dat Corrected typo in torsion: -NH-CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages +N -CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages #### Change log for 2008-05-12 #### -- updated torsion parameters for SM terms CG-CG-SM-CG SM-CG-CG-HC SM-CG-CG-H1 CG-CG-CG-SM CG-CG-SM-CG 1 0.32 0.0 -3. ***G06 Ethyl(methyl)sulfane 1 0.35 0.0 -2. 1 0.35 0.0 1. SM-CG-CG-HC 1 0.08 0.0 3. ***G06 Ethyl(methyl)sulfane SM-CG-CG-H1 1 0.15 0.0 -3. ***G06 2-Methoxyethyl(methyl)sulfane 1 -0.05 0.0 -2 1 0.04 0.0 1 CG-CG-CG-SM 1 0.01 0.0 -3. ***G06 Propyl(methyl)sulfane 1 0.20 0.0 -2. 1 0.51 0.0 1. -- updated the contributors list, added: Austin Yongye Matthew Tessier Sameer Kawatkar File: Parm_Docs/Glycam_06c.txt =================================== #### Change log for 2011-09-15 #### Changed by BLFoley to create Glycam_06c-1.dat Corrected typo in torsion: -NH-CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages +N -CG-CG-SM 1 0.45 0.0 -3. SCEE=1.0 SCNB=1.0 Thiol-linkages ######## information in file prior to 20110915 File: readme/Glycam_06c.txt Added terms for lipids (all copies of existing terms) CP-H2 H2-CP-OS CP-OS-CG CP-CG-N OS-CP-OS H2-CP-CG CG-OS-CP-CG OS-CP-CG-N H2-CP-OS-CG H2-CP-CG-H1 H2-CP-CG-N H2-CP-CG-CG CP-OS-CG-H1 CP-CG-N -H CP-CG-CG-CG CP-CG-CG-N OH-CG-CG-CP CG-CG-CP-CG H1-CG-CP-CG OS-CG-CP-CG OS-CP-OS-CG CP-OS-CG-CG File: Parm_Docs/Glycam_06b.txt =================================== File: readme/Glycam_06b.txt =================================== 20080110 ABY The following terms were added to the Glycam_06a.dat file, found on glycam and also employed by the webtool, to generate Glycam_06b.dat. The Glycam_06b.dat file now contains parameters for modeling lipids. ### Added Terms CP 12.01 sp3 C aliphatic - carbon atom bonded to an oxygen atom bonded to a phosphorus atom CK 12.01 sp2 C alkenes CJ 12.01 sp2 C alkenes for adjacent double bonds HA 1.008 H aliph. bond. to C in alkenes eg CK HP 1.008 H bonded to C next to positively charged group NT 14.01 sp3 N amine group N3 14.01 sp3 N for charged amino groups (Lys, phospholipids, etc) N3-H 434.0 1.010 Parm94 N3-CG 355.0 1.490 Methanaminium (eqm value from crystal avg) CJ-CK 350.9 1.467 CRC manual for 1,3-butadiene OS-CJ 454.5 1.359 copy of OS-CK OS-CK 454.5 1.359 Methoxyethene (JACS 1993, 115, 11921) CJ-CJ 629.0 1.337 copy of CK-CK CK-CK 629.0 1.337 JCC 1996, 17 (5&6),669 CG-CJ 324.0 1.514 copy of CG-CK CG-CK 324.0 1.514 JCC 1996, 17 (5&6),669 CJ-HA 360.0 1.095 copy of CK-HA CK-HA 360.0 1.095 Ethane for alkenes CG-HP 360.0 1.095 Copy of CG-HC NT-H 434.0 1.010 Parm99 NT-CG 352.0 1.470 K calculated from methyl amine (eqm value from crystal average) CG-CP 310.0 1.520 Copy of CG-CG CP-H1 340.0 1.090 Copy of CG-H1 CP-OS 285.0 1.460 Copy of CG-OS H -N3-CG 45.5 109.2 Methanaminium (eqm. value copied from H -NT-CG) H -N3-H 35.0 109.5 Parm94 N3-CG-HP 57.0 109.6 Methanaminium (eqm. value copied from NT-CG-H1) CJ-CG-CK 46.7 111.5 copy of CK-CG-CK CK-CG-CK 46.7 111.5 K calculated from 1,4-pentadiene (value from ED of C2 and CS conformers JACS 1987,109,24,7304-7309 108.9 deg) CJ-CG-CJ 46.7 111.5 copy of CK-CG-CK OS-CJ-HA 65.1 107.5 copy of OS-CK-HA OS-CK-HA 65.1 107.5 K calculated from methoxyethene (value from J Mol Struct 102 (1983) pg 333-345 methoxyethene 108.3 deg) CG-OS-CJ 38.0 107.0 copy of CG-OS-CK CG-OS-CK 38.0 107.0 K calculated from methoxyethene (value from J Mol Struct 28 (1975) pg 193-203 methoxyethene 118.3 deg) OS-CJ-CJ 59.5 119.0 copy of OS-CK-CK OS-CK-CK 59.5 119.0 K calculated from methoxyethene (value from J Mol Struct 28 (1975) pg 193-203 methoxyethene 127.7 deg) CG-CJ-CG 46.1 115.6 copy of CG-CK-CG CG-CK-CG 46.1 115.6 K calculated from 2-methylpropene (eqm value from ED,MW average 115.6 deg) CK-CJ-HA 32.7 126.4 copy of CJ-CK-HA CJ-CK-HA 32.7 126.4 K calculated from 1,3-butadiene (value form ED of 1,3-butadiene 120.9 deg) CK-CJ-CJ 49.4 127.7 copy of CK-CK-CJ CK-CK-CJ 49.4 127.7 K calculated from 1,3-butadiene (eqm value from ED 124.4 deg) HA-CJ-HA 31.3 117.4 copy of HA-CK-HA HA-CK-HA 31.3 117.4 K calculated from ethylene (eqm value from ED,MW average) HA-CJ-CJ 38.2 121.3 copy of HA-CK-CK HA-CK-CK 38.2 121.3 K calculated from ethylene (eqm value from ED,MW average) H1-CG-CJ 56.0 111.5 copy of H1-CG-CK H1-CG-CK 56.0 111.5 Copy of HC-CG-CK HC-CG-CJ 41.4 114.0 copy of HC-CG-CK HC-CG-CK 41.4 114.0 K calculated from propene (eqm value from JMS 1973,17,207-223,ED 111.7 deg) HA-CJ-CG 50.0 114.0 copy of HA-CK-CG HA-CK-CG 50.0 114.0 K calculated from propene (eqm value from ED,MW average) CG-CJ-CJ 47.9 122.5 copy of CG-CK-CK CG-CK-CK 47.9 122.5 K calculated from propene (eqm value from JMS 1973,17,207-223,ED 124.3 deg) CG-CG-CJ 43.0 112.0 copy of CG-CG-CK CG-CG-CK 43.0 112.0 K calculated from but-1-ene (eqm value from JACS 1980,102(7),471) OH-CG-CJ 70.0 107.5 copy of OH-CG-CK OH-CG-CK 70.0 107.5 Copy of OH-CG-CG HP-CG-HP 40.0 109.5 Copy of HC-CG-HC HP-CG-CP 45.0 112.6 Copy of CG-CG-HC HP-CG-CG 45.0 112.6 Copy of CG-CG-HC CG-N3-CG 54.0 111.1 N3-CG-CP 67.0 111.6 Copy of NT-CG-CG N3-CG-CG 67.0 111.6 Copy of NT-CG-CG H -NT-H 35.0 109.5 Copy of H-N3-H (Parm94) H -NT-CG 49.0 109.2 K calculated from methyl amine (eqm value from crystal average) NT-CG-H1 64.0 109.6 K calculated from methyl amine (eqm value from crystal average) NT-CG-CG 67.0 111.6 K calculated from ethyl amine (eqm value from crystal average) CG-NT-CG 54.0 108.1 K calculated from dimethyl amine (eqm value from crystal average) H1-CP-H1 45.00 109.50 Copy of H1-CG-H1 CP-CG-H1 45.00 111.00 Copy of CG-CG-H1 CG-CP-H1 45.00 111.00 Copy of CG-CG-H1 CP-CG-CG 45.00 113.50 Copy of CG-CG-CG OS-CP-CG 70.00 108.50 Copy of OS-CG-CG OS-CG-CP 70.00 108.50 Copy of OS-CG-CG H1-CP-OS 60.00 110.00 Copy of H1-CG-OS H -N3-CG-HP 1 0.13 0.0 3 Methanaminium H -N3-CG-CG 1 0.13 0.0 3 Ethanaminium CK-CG-CG-N 1 0.18 0.0 -3 Lipids, from N-but-3-en-1-ylacetamide 1 0.03 0.0 -2 1 -0.22 0.0 1 CJ-CG-CG-N 1 0.18 0.0 -3 Lipids, copy of CK-CG-CG-N 1 0.03 0.0 -2 1 -0.22 0.0 1 C -CG-CG-CJ 1 -0.42 0.0 -3 Lipids, from 3-buten-1-ol acetate 1 0.33 0.0 -2 1 0.40 0.0 1 C -CG-CG-CK 1 -0.42 0.0 -3 Lipids, from 3-buten-1-ol acetate 1 0.33 0.0 -2 1 0.40 0.0 1 H1-CG-CG-CK 1 0.10 0.0 3 Lipids, copy of HC-CG-CG-CK H1-CG-CG-CJ 1 0.10 0.0 3 Lipids, copy of HC-CG-CG-CJ OH-CG-CG-CK 1 -0.11 0.0 -3 Lipids, from 3-butenol 1 -0.16 0.0 -2 1 -1.06 0.0 1 OH-CG-CG-CJ 1 -0.11 0.0 -3 Lipids, from 3-butenol 1 -0.16 0.0 -2 1 -1.06 0.0 1 OS-CJ-CJ-CG 1 -13.00 0.0 2 copy of OS-CK-CK-CG OS-CK-CK-CG 1 -13.00 0.0 2 Lipids, from 1-propenylmethylether CK-CJ-CJ-HA 1 -15.00 0.0 2 copy of CJ-CK-CK-HA CJ-CK-CK-HA 1 -15.00 0.0 2 CG-OS-CJ-HA 1 0.08 0.0 -3 copy of CG-OS-CK-HA, coupled to CG-OS-CJ-CJ 1 0.22 0.0 -2 1 0.40 0.0 1 CG-OS-CK-HA 1 0.08 0.0 -3 Lipids, from methoxyethene, coupled to CG-OS-CK-CK 1 0.22 0.0 -2 1 0.40 0.0 1 OS-CJ-CJ-HA 1 -20.00 0.0 2 copy of OS-CK-CK-HA OS-CK-CK-HA 1 -20.00 0.0 2 Lipids, from methoxyethene H1-CG-OS-CJ 1 0.10 0.0 3 copy of H1-CG-OS-CK H1-CG-OS-CK 1 0.10 0.0 3 Lipids, from methoxyethene CG-CG-OS-CJ 1 -0.01 0.0 -3 copy of CG-CG-OS-CK 1 -0.42 0.0 -2 1 0.22 0.0 1 CG-CG-OS-CK 1 -0.01 0.0 -3 Lipids, from ethoxyethene 1 -0.42 0.0 -2 1 0.22 0.0 1 CG-OS-CJ-CJ 1 -0.87 0.0 -3 copy of CG-OS-CK-CK 1 -3.99 0.0 -2 1 -0.25 0.0 1 CG-OS-CK-CK 1 -0.87 0.0 -3 1 -3.99 0.0 -2 1 -0.25 0.0 1 CJ-CK-CK-CJ 1 -2.00 0.0 2 CK-CJ-CJ-CK 1 -2.00 0.0 2 CK-CG-CK-CK 1 -0.04 0.0 -3 Lipids, from 1,4-Pentadiene 1 -0.68 0.0 -2 1 -0.21 0.0 1 CJ-CG-CK-CK 1 -0.04 0.0 -3 Copy of CK-CG-CK-CK 1 -0.68 0.0 -2 1 -0.21 0.0 1 CK-CG-CJ-CJ 1 -0.04 0.0 -3 Copy of CK-CG-CK-CK 1 -0.68 0.0 -2 1 -0.21 0.0 1 CJ-CG-CJ-CJ 1 -0.04 0.0 -3 Copy of CK-CG-CK-CK 1 -0.68 0.0 -2 1 -0.21 0.0 1 CK-CG-CK-HA 1 0.31 0.0 -3 Lipids, from 1,4-Pentadiene, coupled to CK-CG-CK-CK 1 0.03 0.0 -2 1 0.05 0.0 1 CJ-CG-CK-HA 1 0.31 0.0 -3 Copy of CK-CG-CK-HA, coupled to CJ-CG-CK-CK 1 0.03 0.0 -2 1 0.05 0.0 1 CK-CG-CJ-HA 1 0.31 0.0 -3 Copy of CK-CG-CK-HA, coupled to CK-CG-CJ-CJ 1 0.03 0.0 -2 1 0.05 0.0 1 CJ-CG-CJ-HA 1 0.31 0.0 -3 Copy of CK-CG-CK-HA, coupled to CJ-CG-CJ-CJ 1 0.03 0.0 -2 1 0.05 0.0 1 CJ-CK-CK-CG 1 -3.50 0.0 2 copy of CK-CJ-CJ-CG CK-CJ-CJ-CG 1 -3.50 0.0 2 Lipids, from CG-CG-CJ-CG 1 -0.01 0.0 -3 copy of CG-CG-CK-CG 1 -0.34 0.0 -2 1 0.29 0.0 1 CG-CG-CK-CG 1 -0.01 0.0 -3 Lipids 1 -0.34 0.0 -2 1 0.29 0.0 1 HC-CG-CJ-CG 1 0.0 0.0 1 copy of HC-CG-CK-CG,no term necessary HC-CG-CK-CG 1 0.0 0.0 1 Lipids, no term necessary HA-CK-CJ-HA 1 0.69 0.0 -3 Lipids - 1,3-butadiene 1 -1.75 0.0 -2 1 0.92 0.0 1 HA-CJ-CK-CK 1 0.17 0.0 -3 copy of HA-CK-CJ-CJ 1 0.40 0.0 -2 1 0.69 0.0 1 HA-CK-CJ-CJ 1 0.17 0.0 -3 Lipids - 1,3-butadiene 1 0.40 0.0 -2 1 0.69 0.0 1 CJ-CJ-CK-CK 1 0.69 0.0 -3 Lipids - adjacent double-bonded carbons 1 -1.75 0.0 -2 1 0.92 0.0 1 OH-CG-CJ-CJ 1 -0.50 0.0 -3 copy of OH-CG-CK-CK 1 -1.00 0.0 -2 1 -0.50 0.0 1 OH-CG-CK-CK 1 -0.50 0.0 -3 Lipids 1 -1.00 0.0 -2 1 -0.50 0.0 1 OH-CG-CJ-HA 1 0.0 0.0 1 Coupled to OH-CG-CK-CK, copy of OH-CG-CK-HA OH-CG-CK-HA 1 0.0 0.0 1 Coupled to OH-CG-CK-CK HO-OH-CG-CJ 1 0.20 0.0 -3 copy of HO-OH-CG-CK 1 0.58 0.0 -2 1 0.38 0.0 1 HO-OH-CG-CK 1 0.20 0.0 -3 Lipids 1 0.58 0.0 -2 1 0.38 0.0 1 CG-CG-CG-CJ 1 0.0 0.0 3 copy of CG-CG-CG-CJ CG-CG-CG-CK 1 0.0 0.0 3 Lipids CG-CG-CJ-CJ 1 -0.5 0.0 -3 copy of CG-CG-CK-CK 1 -0.4 0.0 2 CG-CG-CK-CK 1 -0.5 0.0 -3 Lipids 1 -0.4 0.0 2 CG-CG-CJ-HA 1 0.0 0.0 1 Lipids coupled to CG-CG-CK-CK, copy of CG-CG-CK-HA CG-CG-CK-HA 1 0.0 0.0 1 Lipids coupled to CG-CG-CK-CK CG-CJ-CJ-CG 1 -15.0 0.0 -2 copy of CG-CK-CK-CG 1 0.5 0.0 1 CG-CK-CK-CG 1 -15.0 0.0 -2 Lipids 1 0.5 0.0 1 HC-CG-CG-CJ 1 0.1 0.0 3 copy of HC-CG-CG-CK HC-CG-CG-CK 1 0.1 0.0 3 Lipids H1-CG-CJ-CJ 1 -0.33 0.0 3 Copy of HC-CG-CK-CK H1-CG-CK-CK 1 -0.33 0.0 3 Copy of HC-CG-CK-CK HC-CG-CJ-CJ 1 -0.34 0.0 -3 Copy of HC-CG-CK-CK 1 -0.1 0.0 -2 1 0.1 0.0 1 HC-CG-CK-CK 1 -0.34 0.0 -3 Lipids 1 -0.1 0.0 -2 1 0.1 0.0 1 HC-CG-CJ-HA 1 0.0 0.0 3 Lipids coupled to HC-CG-CJ-CJ HC-CG-CK-HA 1 0.0 0.0 3 Lipids coupled to HC-CG-CK-CK H1-CG-CJ-HA 1 0.0 0.0 3 Copy of HC-CG-CK-HA H1-CG-CK-HA 1 0.0 0.0 3 Copy of HC-CG-CK-HA HA-CJ-CJ-CG 1 -21.0 0.0 2 copy of HA-CK-CK-CG HA-CK-CK-CG 1 -21.0 0.0 2 Lipids HA-CJ-CJ-HA 1 -8.5 0.0 2 copy of HA-CK-CK-HA HA-CK-CK-HA 1 -8.5 0.0 2 Lipids HP-CG-CP-OS 1 0.05 0.0 3. Copy of HC-CG-CG-OS HP-CG-CG-OS 1 0.05 0.0 3. Copy of HC-CG-CG-OS HP-CG-CP-H1 1 0.13 0.0 3. Copy of HC-CG-CG-HC HP-CG-CG-H1 1 0.13 0.0 3. Copy of HC-CG-CG-HC HP-CG-CG-HC 1 0.13 0.0 3. Copy of HC-CG-CG-HC HP-CG-CG-CG 1 0.10 0.0 3. Copy of HC-CG-CG-CG CG-N3-CG-CP 1 0.1 0.0 -3 Copy of CG-N3-CG-CG 1 -0.2 0.0 -2 1 0.1 0.0 1 CG-N3-CG-CG 1 0.1 0.0 -3 N-methylethanaminium 1 -0.2 0.0 -2 1 0.1 0.0 1 CG-NT-CG-CG 1 0.1 0.0 -3 N-Ethyl N-Methyl amine 1 -0.2 0.0 -2 1 0.1 0.0 1 N3-CG-CG-CG 1 0.3 0.0 -3 Propanaminium 1 -0.1 0.0 -2 1 0.1 0.0 1 NT-CG-CG-CG 1 0.3 0.0 -3 N-Propyl amine 1 -0.1 0.0 -2 1 0.1 0.0 1 NT-CG-CG-HC 1 0.1 0.0 3 N-ethyl amine N3-CG-CG-HC 1 0.1 0.0 3 Ethanaminium NT-CG-CG-H1 1 0.1 0.0 3 N-ethyl amine N3-CG-CP-H1 1 0.1 0.0 3 Copy of NT-CG-CG-H1 N3-CG-CG-H1 1 0.1 0.0 3 Copy of NT-CG-CG-H1 NT-CG-CG-OS 1 1.5 0.0 -3 2-Methoxy ethyl amine 1 0.5 0.0 -2 1 -0.5 0.0 1 N3-CG-CP-OS 1 1.5 0.0 -3 2-Methoxyethanaminium 1 0.5 0.0 -2 1 -0.5 0.0 1 N3-CG-CG-OS 1 1.5 0.0 -3 2-Methoxyethanaminium 1 0.5 0.0 -2 1 -0.5 0.0 1 NT-CG-CG-OH 1 0.6 0.0 -3 2-Hydroxy ethyl amine 1 0.5 0.0 -2 1 -1.0 0.0 1 N3-CG-CG-OH 1 0.6 0.0 -3 2-Hydroxyethanaminium 1 0.5 0.0 -2 1 -1.0 0.0 1 HP-CG-N3-CG 1 0.25 0.0 3 Dimethylammonium H1-CG-NT-CG 1 0.25 0.0 3 N,N-Dimethyl amine HC-CG-NT-CG 1 0.25 0.0 3 N,N-Dimethyl amine OS-C -CG-CG 1 0.20 0.0 3 Methyl propanoate CG-CG-NT-H 1 0.2 0.0 3 N-Ethyl amine H1-CG-NT-H 1 0.17 0.0 3 N-Methyl amine NT-CG-CG-HC 1 0.1 0.0 3 ***N-ethyl amine***Awaiting Correction NT-CG-CG-H1 1 0.1 0.0 3 ***N-ethyl amine***Awaiting Correction CP-CG-OS-C 1 -0.04 0.0 -3 Copy of CG-CG-OS-C 1 0.47 0.0 1 H1-CG-CP-H1 1 0.17 0.0 3. Copy of H1-CG-CG-H1 H1-CG-CG-CP 1 0.15 0.0 3. Copy of H1-CG-CG-CG H1-CP-CG-CG 1 0.15 0.0 3. Copy of H1-CG-CG-CG OS-CP-CG-CG 1 -0.27 0.0 1. Copy of OS-CG-CG-CG OS-CG-CG-CP 1 -0.27 0.0 1. Copy of OS-CG-CG-CG CG-OS-CG-CP 1 0.16 0.0 3. Copy of CG-OS-CG-CG OH-CG-CG-HP 1 0.05 0.0 3. Tertbutanol OS-CG-CP-OS 1 0.82 0.0 2. Copy of OS-CG-CG-OS H1-CG-CP-OS 1 0.05 0.0 3. Copy of H1-CG-CG-OS H1-CP-CG-OS 1 0.05 0.0 3. Copy of H1-CG-CG-OS H1-CG-CP-OS 1 0.05 0.0 3. Copy of H1-CG-CG-OS HA 1.4590 0.0150 Spellmeyer HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 CP 1.9080 0.1094 Spellmeyer CK 1.9080 0.0860 Spellmeyer CJ 1.9080 0.0860 Spellmeyer NT 1.8240 0.1700 OPLS N3 1.8240 0.1700 OPLS ### Term Discrepencies N -C -CG-OH 1 0.1 0.0 -3 2-Hydroxy ethanamide 1 -2.2 0.0 -2 1 2.0 0.0 1 ### Other Issues # Missing from glycam web file, but not mine N -C -CG-CG 1 0.20 0.0 -3 Propanamide 1 -0.70 0.0 -2 1 0.05 0.0 1 O -C -CG-CG 1 0.50 0.0 -3 Propanamide (coupled to N -C -CG-CG) 1 -0.10 0.0 -2 1 -0.05 0.0 1 # Terms are in glycam web file, but incorrectly assigned (C next to P is CP) H1-CP-OS-P 1 0.07 0.0 3. Dimethyl phosphate OS-P -OS-CP 1 0.50 0.0 -3. Dimethyl phosphate 1 0.70 0.0 2. O2-P -OS-CP 1 0.10 0.0 -3. Dimethyl phosphate 1 -0.50 0.0 -2. 1 0.10 0.0 1 P -OS-CP-CG 1 0.10 0.0 -3 Methyl ethyl phosphate 1 0.05 0.0 -2 1 -1.20 0.0 1 H2-CP-OS-P 1 0.07 0.0 3. Dimethyl phosphate OS-CP-OS-P 1 0.40 0.0 -3 Methoxy methyl methyl phosphate 1 0.40 0.0 -2 1 -0.50 0.0 1 File: Parm_Docs/Glycam_06a.txt =================================== The following parameters were added to Glycam_06.dat to make Glycam_06a.dat The phosphate valence terms were adopted from Parm94.dat S 32.06 sulphur in sulphates ABY 03/15/05 P 30.97 phosphate in phosphates ABY 04/24/05 Bonds: P -OS 230.0 1.610 Parm94 P -O2 525.0 1.480 Parm94 S -OS 206.0 1.589 K calculated from methyl sulphate (eqm value from THEOCHEM 395/396 (1997) 107-122) S -O2 620.0 1.440 K calculated from methyl sulphate (eqm value from THEOCHEM 395/396 (1997) 107-122) Angles: OS-P -OS 45.0 102.6 Parm94 P -OS-CG 50.0 121.0 K calculated from dimethyl phosphate (eqm value from crystal average) O2-P -OS 100.0 108.2 Parm94 O2-P -O2 140.0 119.9 Parm94 O2-S -O2 123.0 113.91 K calculated from methyl sulphate (eqm value from THEOCHEM 395/396 (1997) 107-122) S -OS-CG 50.0 118.88 K calculated from methyl sulphate (eqm value from THEOCHEM 395/396 (1997) 107-122) O2-S -OS 104.0 106.87 K calculated from methyl sulphate (eqm value from THEOCHEM 395/396 (1997) 107-122) OH-CG-C 63.00 112.36 Glycam_93 (taken from OS-CG-C) - for N-glycolyl Dihedral angles: C -CG-OH-HO 1 0.9 0.0 2 2-Hydroxy ethanamide O -C -CG-H1 1 0.0 0.0 3 2-Hydroxy ethanamide N -C -CG-H1 1 0.0 0.0 3 2-Hydroxy ethanamide (coupled to O -C -CG-H1) N -C -CG-OH 1 0.20 0.0 -3 2-Hydroxy ethanamide 1 -2.21 0.0 -2 1 2.24 0.0 1 O -C -CG-OH 1 0.0 0.0 3 2-Hydroxy ethanamide (coupled to N -C -CG-OH) H1-CG-OS-P 1 0.07 0.0 3. Dimethyl phosphate OS-P -OS-CG 1 0.50 0.0 -3. Dimethyl phosphate 1 0.70 0.0 2. O2-P -OS-CG 1 0.10 0.0 -3. Dimethyl phosphate 1 -0.50 0.0 -2. 1 0.10 0.0 1 P -OS-CG-CG 1 0.10 0.0 -3 Methyl ethyl phosphate 1 0.05 0.0 -2 1 -1.20 0.0 1 H2-CG-OS-P 1 0.07 0.0 3. Dimethyl phosphate OS-CG-OS-P 1 0.40 0.0 -3 Methoxy methyl methyl phosphate 1 0.40 0.0 -2 1 -0.50 0.0 1 CG-OS-S -O2 1 0.18 0.0 3. Methyl sulphate - CH3OSO3 H1-CG-OS-S 1 0.17 0.0 3. Methyl sulphate -CH3CH2OSO3 CG-CG-OS-S 1 -1.20 0.0 1. Ethyl sulphate - CH3OSO3 van der Waals S 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's 03/16/05 from parm94.dat P 2.1000 0.2000 JCC,7,(1986),230; 04/24/05 from parm94.dat