dendrimer builder
Hi!
A few weeks ago I asked about a dendrimer coordinate
builder suitable to generate initial coordinates
for MM/MD simulations.
I received a few suggestions, and a few requests for
the answers. Unfortunately, no builder is currently
available, so I went ahead and programmed one taking
advantage of the coordinate manipulation features
of Charmm. I first must thank those who submitted
suggestions, and the support people from MSI who
rebuilt my original patch!
For the benefit of those who requested it, I am
appending the rtf and Charmm script file at the
end of this file.
The rtf file below supports the
necessary patches to construct a PAMAM starburst
dendrimer with a NH3 core. If you write your own
patches, the Charmm script is "generic" enough
that you should be able to construct different starburst dendrimers
with a different core, or repeat unit.
In a nutshell, the Charmm script below computes the
necessary offsets so that the correct indeces
in the linear sequence of repeat
units (specified by the SEQUENCE command) are used
to generate the links that build the dendrimer. The links
are generated using the patching mechanism of Charmm.
The difficulty with programs that expect a linear polymer like the
amino acid sequence of a protein is that making the
apropriate links between different residues can be
confusing. If anybody is interested in details of the
script (ie. reference to the equations, etc.), please
e-mail me directly.
Finally, some caveats:
1) the rtf is suitable to construct the coordinates.
There may be some holes in the description of the
internal coordinates that define the force field,
ie. an improper dihedral may not be specified etc.
2) the script and the rtf have only been tested under Charmm 23.1
as supplied under Quanta 4.1.1 by MSI, and with an
older parm file, PARM22.
3) the amidoamine unit (AMT) is defined in its extended
and trans form.
4) it may be appropriate to sequentially build the dendrimer
with minimization or dynamic runs relaxing the system as
you build successive generations. This will require
modifying the script, but this is not too difficult.
5) i don't claim that the algorithm below is the most
efficient way of doing this! I am sure some graph theory
inclined people can do a much better job!
Bye and Good Luck!
******* Charmm script *******
* PAMAM dendrimer coordinate builder
* written by Gustavo A. Mercier, Jr.
* NIH/LDRR 4/96
* ... Example G=3
*
bomb -2
! UPPER
! read the dendrimer rtf and a parameter file
read rtf card name dd.rtf
read para card name parm.prm
! Here we define the variables that define the dendrimer
set Nc 3 ! Number of branches in the core
set Ng 3 ! Number of Generations = 2
set Nb 2 ! Branches at Branchpoint = Nb = 2
! Here we initialize other variables
set NRb 0 ! Total number of Residues in the branch; computed below
set Zp 1 ! Branchpoints at the periphery = Zp = 1
set Of1 0 ! Offset1 to move over residues to patch a branchpoint
! Number of residues used up to Ng-2
set Of2 0 ! Offset2 to move over branchpoints
! Number of residues used up to Ng-1
set iNc 1 ! Counter for the number of branches in the core
set iNg 1 ! Counter for the generations = g
set iNb 1 ! Counter for the branchpoints
set iRh 0 ! Residue index of the head = ri
! Here you specify variables for each residue that attaches to the head
! in your patch; We assume that one patch makes all the necessary
! changes at a branchpoint. Otherwise, you would have to loop
! over the patches, and take appropriate care over the indeces of
! the residues; In the PAMAM case the patch DEND uses 2 residues
! as tails to one head.
set iRt1 0 ! Residue index of the tail 1
set iRt2 0 ! Residue index of the tail 2
! Here we initialize storage variables
set sto1 0 ! storage
set sto2 0 ! storage
! First, generate the three branches
! individually so that the residues of a branch
! are together in the output coordinate file
! Successive branches have segid = # of branch
! Total number of residues in a branch
LET sto1 = -8 at 8- Ng + 1
LET sto2 = -8 at 8- Nb ** -8 at 8- sto1
LET sto2 = -8 at 8- sto2 - 1
LET sto1 = -8 at 8- Nb - 1
LET NRb = -8 at 8- sto2 / -8 at 8- sto1
LABEL L_CORE
READ SEQU AMT -8 at 8- NRb
GENE -8 at 8- iNc SETUP
! patch the branch
LABEL L_GEN
! CALC Zp ( -8 at 8- Nb ) ** ( ( -8 at 8- iNg ) - 1 )
LET Zp = -8 at 8- iNg - 1
LET Zp = -8 at 8- Nb ** -8 at 8- Zp
! CALC Of2 ( -8 at 8- Zp - 1 ) / ( -8 at 8- Nb - 1 )
LET sto1 = -8 at 8- Zp - 1
LET sto2 = -8 at 8- Nb - 1
DIVI sto1 BY -8 at 8- sto2 ! This is done to avoid some bug with LET
SET Of2 -8 at 8- sto1
! CALC Of1 ( ( ( -8 at 8- Nb ) * ( -8 at 8- Zp ) ) - 1 ) / ( -8 at 8- Nb -
1 )
LET sto1 = -8 at 8- Nb * -8 at 8- Zp
LET sto1 = -8 at 8- sto1 - 1
LET sto2 = -8 at 8- Nb - 1
LET Of1 = -8 at 8- sto1 / -8 at 8- sto2
LABEL L_BRANP
! CALC iRh -8 at 8- Of2 + -8 at 8- iNb
LET iRh = -8 at 8- Of2 + -8 at 8- iNb
! CALC iRt1 -8 at 8- Of1 + 1
LET iRt1 = -8 at 8- Of1 + 1
! CALC iRt2 -8 at 8- Of1 + 2
LET iRt2 = -8 at 8- Of1 + 2
PATCH DEND -8 at 8- iNc -8 at 8- iRh -8 at 8- iNc -8 at 8- iRt1 -8
at 8- iNc -8 at 8- iRt2 SETUP
SET Of1 -8 at 8- iRt2
INCR iNb BY 1
IF -8 at 8- iNb GT -8 at 8- Zp THEN GOTO E_BRANP
GOTO L_BRANP
LABEL E_BRANP
SET iNb 1 ! reset the counter
INCR iNg BY 1
IF -8 at 8- iNg GT -8 at 8- Ng THEN GOTO E_GEN
GOTO L_GEN
LABEL E_GEN
SET iNg 1
INCR iNc BY 1
IF -8 at 8- iNc GT -8 at 8- Nc THEN GOTO E_CORE
GOTO L_CORE
LABEL E_CORE
! Now link to the core; here it is NH3
READ SEQU card
* NH3
*
1
NH3
GENE 0 SETUP
PATCH NGZ 0 1 1 1 2 1 3 1 SETUP
! Now generate the coordinates
IC PARA
IC SEED 0 1 N 1 1 C1 1 1 C2
IC BUILD
IC FILL
print ic
print coor
write coor card name "test.crd"
* PAMAM g3 NH3 core
*
! You could write a PSF if you wanted to!
! write psf card name "test.PSF"
! * PAMAM g3 NH3 core
! *
STOP
******* End of Charmm script ********
******* Begin rtf ********
* Topology file containing the dendrimer units
* ...
* ... 4/25/96 Modified by G. Mercier M.D.,Ph.D..
* ... Original by G. Mercier, but DEND patch written
* ... by Dr. Funchness of support at msi.com (4/24/96)
* ...
* sorted alphabetically; metals follow organics
* Atom type numbers 201-229 are reserved for special QUANTA display atom types.
* Last current active number is 234.
*
22 0
MASS 170 AR 39.948 Ar ! Argon
MASS 7 B 10.81 B ! Boron
MASS 14 C 12.01100 C ! Carbonyl or Guanidinium carbon
MASS 190 C3 12.01100 C ! Carbonyl carbon in 3-membered aliphatic ring
MASS 192 C4 12.01100 C ! Carbonyl carbons in 4-membered aliphatic ring
MASS 21 C5R 12.01100 C ! Aromatic carbon in a five membered ring
MASS 23 C5RE 13.01900 C ! Extended aromatic carbon in five membered ring
MASS 28 C5RP 12.01100 C ! for Aryl-Aryl bond between C5R rings
MASS 189 C5RQ 12.01100 C ! for second Ar-Ar bond between C5RP rings (ortho)
MASS 22 C6R 12.01100 C ! Aromatic carbon in a six membered ring
MASS 24 C6RE 13.01900 C ! Extended aromatic carbon in six membered ring
MASS 29 C6RP 12.01100 C ! for Aryl-Aryl bond between C6R rings
MASS 194 C6RQ 12.01100 C ! Carbon of C6RP type ortho to C6RP pair
MASS 230 CF1 12.01100 C ! Carbon with one Fluorine
MASS 231 CF2 12.01100 C ! Carbon with two Fluorines
MASS 232 CF3 12.01100 C ! Carbons with three Fluorines
MASS 11 CH1E 13.01900 C ! Extended atom carbon with one hydrogen
MASS 12 CH2E 14.02700 C ! Extended atom carbon with two hydrogens
MASS 13 CH3E 15.03500 C ! Extended atom carbon with three hydrogens
MASS 15 CM 12.01100 C ! Carbonmonoxide, or other triply bonded, carbon
MASS 199 CP3 12.01100 C ! Carbon on nitrogen in proline ring
MASS 197 CPH1 12.01100 C ! CG and CD2 carbons in histidine ring
MASS 198 CPH2 12.01100 C ! CE1 carbon in histidine ring
MASS 195 CQ66 12.01100 C ! Third adjacent pair of CR66 types in fused rings
MASS 25 CR55 12.01100 C ! Aromatic carbon-merged five membered rings
MASS 26 CR56 12.01100 C ! Aromatic carbon-merged five/six membered rings
MASS 27 CR66 12.01100 C ! Aromatic carbon-merged six membered rings
MASS 196 CS66 12.01100 C ! Second adjacent pair of CR66 types in fused rings
MASS 10 CT 12.01100 C ! Aliphatic carbon (tetrahedral)
MASS 191 CT3 12.01100 C ! in 3-membered aliphatic ring, usually tetrahedral
MASS 193 CT4 12.01100 C ! in 4-membered aliphatic ring, usually tetrahedral
MASS 16 CUA1 12.01100 C ! Carbon in double bond, first pair
MASS 17 CUA2 12.01100 C ! Carbon in double bond, second conjugated pair
MASS 20 CUA3 12.01100 C ! Carbon in double bond, third conjugated pair
MASS 18 CUY1 12.01100 C ! Carbon in triple bond, first pair
MASS 19 CUY2 12.01100 C ! Carbon in triple bond, second conjugated pair
MASS 1 H 1.00800 H ! Hydrogen bonding hydrogen (neutral group)
MASS 3 HA 1.00800 H ! Aliphatic or aromatic hydrogen
MASS 2 HC 1.00800 H ! Hydrogen bonding hydrogen (charged group)
MASS 168 HE 4.00260 He ! Helium
MASS 9 HMU 1.00800 H ! Mu-bonded hydrogen for metals and boron-hydride
MASS 8 HO 1.00800 H ! Hydrogen on an alcohol oxygen
MASS 4 HT 1.00800 H ! TIPS3P water model hydrogen
MASS 171 KR 83.80 Kr ! Krypton
MASS 5 LP 0.0 ! ST2 lone pair
MASS 31 N 14.00670 N ! Nitrogen; planar-valence of 3, i.e. nitrile, etc.
MASS 234 N3 14.00670 N ! Nitrogen in a three membered ring
MASS 34 N5R 14.00670 N ! Nitrogen in a five membered aromatic ring
MASS 30 N5RP 14.00670 N ! for Ar-Ar bond between five membered rings
MASS 35 N6R 14.00670 N ! Nitrogen in a six membered aromatic ring
MASS 39 N6RP 14.00670 N ! for Aryl-Aryl bond between six membered rings
MASS 37 NC 14.00670 N ! Charged guanidinium-type nitrogen
MASS 186 NC2 14.00670 N ! for neutral guanidinium group - Arg sidechain
MASS 169 NE 20.179 Ne ! Neon
MASS 38 NO2 14.00670 N ! Nitrogen in nitro, or related, group
MASS 32 NP 14.00670 N ! Nitrogen in peptide, amide, or related, group
MASS 183 NR1 14.00670 N ! Protonated nitrogen in neutral histidine ring
MASS 184 NR2 14.00670 N ! Unprotonated nitrogen in neutral histidine ring
MASS 185 NR3 14.00670 N ! Nitrogens in charged histidine ring
MASS 182 NR55 14.00670 N ! N at fused bond between two 5-membered aromatics
MASS 180 NR56 14.00670 N ! N at fused bond between 5 and 6-membered aryls
MASS 181 NR66 14.00670 N ! N at fused bond between two 6-membered aromatics
MASS 36 NT 14.00670 N ! Nitrogen (tetrahedral), i.e. Amine, etc.
MASS 33 NX 14.00670 N ! Proline nitrogen, or similar
MASS 40 O 15.99940 O ! Carbonyl oxygen for amides, or related structures
MASS 56 O2M 15.99940 O ! Oxygen in Si-O-Al or Al-O-Al bond
MASS 52 O5R 15.99940 O ! Oxygen in 5 membered aromatic ring-radicals, etc.
MASS 53 O6R 15.99940 O ! Oxygen in 6 membered aromatic ring-radicals, etc.
MASS 41 OA 15.99940 O ! Carbonyl oxygen for aldehydes, or related
MASS 51 OAC 15.99940 O ! Carbonyl oxygen for acids, or related
MASS 43 OC 15.99940 O ! Charged oxygen
MASS 50 OE 15.99940 O ! Ether oxygen / Acetal oxygen
MASS 47 OH2 15.99940 O ! ST2 water model oxygen
MASS 42 OK 15.99940 O ! Carbonyl oxygen for ketones, or related
MASS 48 OM 15.99940 O ! Carbonmonoxide, or other triply bonded, oxygen
MASS 49 OS 15.99940 O ! Ester oxygen
MASS 57 OSH 0.00000 O ! Massless O for zeolites, or related cage cmpds.
MASS 55 OSI 15.99940 O ! Oxygen in Si-O-Si bond
MASS 45 OT 15.99940 O ! Hydroxyl oxygen (tetrahedral) or Ionizable acid
MASS 46 OW 15.99940 O ! TIP3P water model oxygen
MASS 64 P6R 30.9738 P ! Phosphorous in aromatic 6-membered ring
MASS 61 PO3 30.9738 P ! Phosphorous bonded to three oxygens
MASS 62 PO4 30.9738 P ! Phosphorous bonded to four oxygens
MASS 60 PT 30.9738 P ! Phosphorous, general; usually tetrahedral
MASS 63 PUA1 30.9738 P ! Phosphorous double bond
MASS 233 PUY1 30.9738 P ! Triple bonded phosphorus
MASS 173 RN 222.0 Rn ! Radon
MASS 72 S5R 32.0600 S ! Sulphur in a five membered aromatic ring
MASS 73 S6R 32.0600 S ! Sulphur in a six membered aromatic ring
MASS 74 SE 32.060 S ! Thioether sulphur
MASS 71 SH1E 33.06800 S ! Extended atom sulphur with one hydrogen
MASS 75 SK 32.060 S ! Thioketone sulphur
MASS 76 SO1 32.0600 S ! Sulphur bonded to one oxygen
MASS 77 SO2 32.0600 S ! Sulphur bonded to two oxygens
MASS 78 SO3 32.0600 S ! Sulphur bonded to three oxygens
MASS 79 SO4 32.0600 S ! Sulphur bonded to four oxygens
MASS 70 ST 32.06000 S ! Sulphur, general; usually tetrahedral
MASS 131 XAT 210.0 At ! Astatine
MASS 94 XBR 79.904 Br ! Bromine
MASS 93 XCL 35.45300 Cl ! Chlorine
MASS 172 XE 131.29 Xe ! Xenon
MASS 92 XF 18.99840 F ! Fluorine
MASS 95 XI 126.9045 I ! Iodine
MASS 126 MAC 227.0278 Ac ! Actinium
MASS 111 MAG 107.868 Ag ! Silver
MASS 91 MAL 26.9815 Al ! ALuminum
MASS 159 MAM 243.0 Am ! Americium
MASS 101 MAS 74.9216 As ! Arsenic
MASS 119 MAU 196.08 Au ! Gold
MASS 115 MBA 137.33 Ba ! Barium
MASS 6 MBE 9.01218 Be ! Beryllium
MASS 122 MBI 208.9804 Bi ! Bismuth
MASS 161 MBK 247.0 Bk ! Berkelium
MASS 84 MCA 40.080 Ca ! Calcium
MASS 112 MCD 112.41 Cd ! Cadmium
MASS 124 MCE 140.12 Ce ! Cerium
MASS 162 MCF 251.0 Cf ! Californium
MASS 160 MCM 247.0 Cm ! Curium
MASS 99 MCO 58.9332 Co ! Cobalt
MASS 98 MCR 51.996 Cr ! Chromium
MASS 89 MCS 132.9054 Cs ! Cesium
MASS 96 MCU 63.546 Cu ! Copper
MASS 150 MDY 162.50 Dy ! Dysprosium
MASS 152 MER 167.26 Er ! Erbium
MASS 163 MES 252.0 Es ! Einsteinium
MASS 147 MEU 151.96 Eu ! Europium
MASS 86 MFE 55.847 Fe ! Iron
MASS 164 MFM 257.0 Fm ! Fermium
MASS 142 MFR 223.0 Fr ! Francium
MASS 135 MGA 69.72 Ga ! Gallium
MASS 148 MGD 157.25 Gd ! Gadolinium
MASS 136 MGE 72.59 Ge ! Germanium
MASS 175 MHA 262.0 Ha ! Hahnium
MASS 138 MHF 178.49 Hf ! Hafnium
MASS 120 MHG 200.59 Hg ! Mercury
MASS 151 MHO 164.9304 Ho ! Holmium
MASS 137 MIN 114.82 In ! Indium
MASS 140 MIR 192.22 Ir ! Iridium
MASS 83 MK 39.098 K ! Potassium
MASS 123 MLA 138.9055 La ! Lanthanum
MASS 80 MLI 6.941 Li ! Lithium
MASS 167 MLR 260.0 Lr ! Lawrencium
MASS 155 MLU 174.967 Lu ! Lutetium
MASS 165 MMD 258.0 Md ! Medelevium
MASS 82 MMG 24.305 Mg ! Magnesiun
MASS 85 MMN 54.938 Mn ! Manganese
MASS 107 MMO 95.94 Mo ! Molybdenum
MASS 81 MNA 22.9898 Na ! Sodium
MASS 106 MNB 92.9064 Nb ! Niobium
MASS 144 MND 144.24 Nd ! Neodymium
MASS 100 MNI 58.69 Ni ! Nickel
MASS 166 MNO 259.0 No ! Nobelium
MASS 157 MNP 237.0482 Np ! Neptunium
MASS 117 MOS 190.2 Os ! Osmium
MASS 156 MPA 231.0359 Pa ! Protactinium
MASS 121 MPB 207.2 Pb ! Lead
MASS 110 MPD 106.42 Pd ! Palladium
MASS 145 MPM 145.0 Pm ! Promethium
MASS 130 MPO 209.0 Po ! Polonium
MASS 125 MPR 140.9077 Pr ! Praseodymium
MASS 118 MPT 195.08 Pt ! Platinum
MASS 158 MPU 244.0 Pu ! Plutonium
MASS 143 MRA 226.0254 Ra ! Radium
MASS 88 MRB 85.4678 Rb ! Rubidium
MASS 176 MRE 186.31 Re ! Rhenium
MASS 174 MRF 261.0 Rf ! Rutherfordium/Kurchatovium
MASS 109 MRH 102.9055 Rh ! Rhodium
MASS 108 MRU 101.07 Ru ! Ruthenium
MASS 114 MSB 121.75 Sb ! Antimony
MASS 133 MSC 44.9559 Sc ! Scandium
MASS 102 MSE 78.96 Se ! Selenium
MASS 90 MSI 28.0855 Si ! Silicon
MASS 177 MSIU 28.08550 Si ! Silicon when as double bond
MASS 146 MSM 150.36 Sm ! Samarium
MASS 113 MSN 118.69 Sn ! Tin
MASS 103 MSR 87.62 Sr ! Strontium
MASS 139 MTA 180.9479 Ta ! Tantalum
MASS 149 MTB 158.9254 Tb ! Terbium
MASS 132 MTC 98.0 Tc ! Technetium
MASS 129 MTE 127.60 Te ! Tellurium
MASS 127 MTH 232.0381 Th ! Thorium
MASS 134 MTI 47.88 Ti ! Titanium
MASS 141 MTL 204.383 Tl ! Thallium
MASS 153 MTM 168.9342 Tm ! Thulium
MASS 128 MU 238.0289 U ! Uranium
MASS 97 MV 50.9415 V ! Vanadium
MASS 116 MW 183.85 W ! Tungsten
MASS 104 MY 88.9059 Y ! Yttrium
MASS 154 MYB 173.04 Yb ! Ytterbium
MASS 87 MZN 65.38 Zn ! Zinc
MASS 105 MZR 91.22 Zr ! Zirconium
! Autogenerate all angles during generation of the PSF
! AUTOGENERATE ANGLES DIHEDRALS
! Apply terminal patches NONE and NONE by default during
! generation of the PSF
DEFA FIRS NONE LAST NONE
!
! NH3
RESI NH3
GROUP
ATOM N NT -0.30
ATOM H1 H 0.10
ATOM H2 H 0.10
ATOM H3 H 0.10
DONO H1 N
DONO H2 N
DONO H3 N
ACCE N H1
BOND N H1 N H2 N H3
THET H1 N H2 H1 N H3 H2 N H3
IMPH H3 H2 N H1
IC H3 H2 *N H1 0.000 0.0 120.0 0.0 0.00
! The AMT molecule
RESI AMT 0.00
GROUP
ATOM C1 CT -0.15
ATOM H1 HA 0.05
ATOM H2 HA 0.05
ATOM H12 HA 0.05
GROUP
ATOM C2 CT -0.05
ATOM H3 HA 0.05
ATOM H4 HA 0.05
ATOM C3 C 0.60
ATOM O1 O -0.55
ATOM N1 NP -0.40
ATOM H5 H 0.25
ATOM C4 CT -0.05
ATOM H6 HA 0.05
ATOM H7 HA 0.05
GROUP
ATOM C5 CT -0.10
ATOM H8 HA 0.05
ATOM H9 HA 0.05
GROUP
ATOM N2 NT -0.30
ATOM H10 H 0.15
ATOM H11 H 0.15
BOND C1 H12 C1 H1 C1 H2
BOND C1 C2 C2 H3 C2 H4 C2 C3
BOND C3 O1 C3 N1
BOND N1 H5 N1 C4
BOND C4 H6 C4 H7 C4 C5
BOND C5 H9 C5 H8 C5 N2
BOND N2 H10 N2 H11
! IMPH N1 C3 C4 H5
! my impropers
IMPH H1 C2 C1 H2
IMPH H1 C2 C1 H12
IMPH H3 C1 C2 H4
IMPH H3 C1 C2 C3
IMPH O1 C2 C3 N1
IMPH H5 C3 N1 C4
IMPH H6 N1 C4 H7
IMPH H6 N1 C4 C5
IMPH H8 C4 C5 N2
IMPH H8 C4 C5 N2
IMPH H10 C5 N2 H11
!
DONO H5 N1
ACCE O1 C3
IC C1 C2 C3 N1 0.000 0.0 180.0 0.0 0.000
IC C1 C2 C3 O1 0.000 0.0 0.0 0.0 0.000
IC C2 C3 N1 C4 0.000 0.0 180.0 0.0 0.000
IC C3 N1 C4 C5 0.000 0.0 180.0 0.0 0.000
IC N1 C4 C5 N2 0.000 0.0 180.0 0.0 0.000
IC C3 C2 C1 H1 0.000 0.0 60.0 0.0 0.000
IC C3 C2 C1 H2 0.000 0.0 -60.0 0.0 0.000
IC N1 C3 C2 H3 0.000 0.0 60.0 0.0 0.000
IC N1 C3 C2 H4 0.000 0.0 -60.0 0.0 0.000
IC O1 C3 N1 H5 0.000 0.0 180.0 0.0 0.000
IC C3 N1 C4 H6 0.000 0.0 -60.0 0.0 0.000
IC C3 N1 C4 H7 0.000 0.0 60.0 0.0 0.000
IC N1 C4 C5 H8 0.000 0.0 -60.0 0.0 0.000
IC N1 C4 C5 H9 0.000 0.0 60.0 0.0 0.000
IC C4 C5 N2 H10 0.000 0.0 120.0 0.0 0.000
IC C4 C5 N2 H11 0.000 0.0 -120.0 0.0 0.000
IC C3 C2 C1 H12 0.000 0.0 180.0 0.0 0.000
! Patch to generate the g0 core in
! NH3 core PAMAM
! residue 1 is the NH3 core
! residue 2 is C1 head one
! residue 3 is C1 head two
! residue 4 is C1 head three
!
! 2C1----
! /
! 1N-----------3C1-------
! \
! 4C1----
PRES NGZ
ATOM 1N NT -0.15
ATOM 2C1 CT -0.05
ATOM 2H1 HA 0.05
ATOM 2H2 HA 0.05
ATOM 3C1 CT -0.05
ATOM 3H1 HA 0.05
ATOM 3H2 HA 0.05
ATOM 4C1 CT -0.05
ATOM 4H1 HA 0.05
ATOM 4H2 HA 0.05
DELE ATOM 1H1
DELE ATOM 1H2
DELE ATOM 1H3
DELE ATOM 2H12
DELE ATOM 3H12
DELE ATOM 4H12
BOND 1N 2C1 1N 3C1 1N 4C1
THET 2C1 1N 3C1
THET 2C1 1N 4C1
THET 3C2 1N 4C1
THET 1N 2C1 2C2
THET 1N 3C1 3C2
THET 1N 4C1 4C2
THET 1N 2C1 2H1
THET 1N 2C1 2H2
THET 1N 3C1 3H1
THET 1N 3C1 3H2
THET 1N 4C1 4H1
THET 1N 4C1 4H2
DIHE 3C1 1N 2C1 2H1
DIHE 3C1 1N 2C1 2H2
DIHE 3C1 1N 2C1 2C2
DIHE 2C1 1N 3C1 3H1
DIHE 2C1 1N 3C1 3H2
DIHE 2C1 1N 3C1 3C2
DIHE 3C1 1N 4C1 4H1
DIHE 3C1 1N 4C1 4H2
DIHE 3C1 1N 4C3 4C2
DIHE 1N 2C1 2C2 2H3
DIHE 1N 2C1 2C2 2H4
DIHE 1N 2C1 2C2 2C3
DIHE 1N 3C1 3C2 3H3
DIHE 1N 3C1 3C2 3H4
DIHE 1N 3C1 3C2 3C3
DIHE 1N 4C1 4C2 4H3
DIHE 1N 4C1 4C2 4H4
DIHE 1N 4C1 4C2 4C3
IMPH 4C1 3C1 1N 2C1
IMPH 2H1 1N 2C1 2H2
IMPH 2H1 1N 2C1 2C2
IMPH 3H1 1N 3C1 3H2
IMPH 3H1 1N 3C1 3C2
IMPH 4H1 1N 4C1 4H2
IMPH 4H1 1N 4C1 4C2
IC 4C1 3C1 *1N 2C1 0.000 0.0 120.0 0.0 0.000
IC 3C1 1N 2C1 2C2 0.000 0.0 -60.0 0.0 0.000
IC 1N 2C1 2C2 2C3 0.000 0.0 180.0 0.0 0.000
IC 2C2 2C1 1N 3C1 0.000 0.0 120.0 0.0 0.000
IC 2C1 1N 3C1 3C2 0.000 0.0 90.0 0.0 0.000
IC 1N 3C1 3C2 3C3 0.000 0.0 180.0 0.0 0.000
IC 2C2 2C1 1N 4C1 0.000 0.0 -120.0 0.0 0.000
IC 2C1 1N 4C1 4C2 0.000 0.0 180.0 0.0 0.000
IC 1N 4C1 4C2 4C3 0.000 0.0 180.0 0.0 0.000
! PAMAM patch to connect to N2 as follows
! residue 1 is the N2 tail
! residue 2 is the C1 head one
! resiude 3 is the C1 head two
! 2C1----
! /
! ---1N2
! \
! 3C1----
PRES DEND
DELE ATOM 1H10
DELE ATOM 1H11
DELE ATOM 2H12
DELE ATOM 3H12
GROUP
ATOM 1N2 NT -0.10
ATOM 2C1 CT -0.05
ATOM 2H1 HA 0.05
ATOM 2H2 HA 0.05
ATOM 3C1 CT -0.05
ATOM 3H1 HA 0.05
ATOM 3H2 HA 0.05
BOND 1N2 2C1
BOND 1N2 3C1
THET 1C5 1N2 2C1
THET 1N2 2C1 2C2
THET 1N2 2C1 2H1
THET 1N2 2C1 2H2
THET 1C5 1N2 3C1
THET 1N2 3C1 3C2
THET 1N2 3C1 3H1
THET 1N2 3C1 3H2
THET 2C1 1N2 3C1
DIHE 1C4 1C5 1N2 2C1
DIHE 1H8 1C5 1N2 2C1
DIHE 1H9 1C5 1N2 2C1
DIHE 1C4 1C5 1N2 3C1
DIHE 1H8 1C5 1N2 3C1
DIHE 1H9 1C5 1N2 3C1
DIHE 1C5 1N2 2C1 2C2
DIHE 1C5 1N2 2C1 2H1
DIHE 1C5 1N2 2C1 2H2
DIHE 1C5 1N2 3C1 3C2
DIHE 1C5 1N2 3C1 3H1
DIHE 1C5 1N2 3C1 3H2
DIHE 1N2 2C1 2C2 2C3
DIHE 1N2 2C1 2C2 2H3
DIHE 1N2 2C1 2C2 2H4
DIHE 1N2 3C1 3C2 3C3
DIHE 1N2 3C1 3C2 3H3
DIHE 1N2 3C1 3C2 3H4
DIHE 2C2 2C1 1N2 3C1
DIHE 2H1 2C1 1N2 3C1
DIHE 2H2 2C1 1N2 3C1
DIHE 2C1 1N2 3C1 3C2
DIHE 2C1 1N2 3C1 3H1
DIHE 2C1 1N2 3C1 3H2
! my impropers
IMPH 2H1 2C2 2C1 1N2
IMPH 3H1 3C2 3C1 1N2
IMPH 2C1 1C5 1N2 3C1
IMPH 2H1 1N2 2C1 2H2
IMPH 2H1 1N2 2C1 2C2
IMPH 3H1 1N2 3C1 3H2
IMPH 3H1 1N2 3C1 3C2
!
! 2C2 dihedral is 90 rather than 180 to allow for tilt into
! H-bonding position upon minimization/dynamics
IC 1C4 1C5 1N2 2C1 0.000 0.0 120.0 0.0 0.000
IC 1C4 1C5 1N2 3C1 0.000 0.0 -120.0 0.0 0.000
IC 1C5 1N2 2C1 2C2 0.000 0.0 090.0 0.0 0.000
IC 1N2 2C1 2C2 2C3 0.000 0.0 180.0 0.0 0.000
IC 1C5 1N2 3C1 3C2 0.000 0.0 180.0 0.0 0.000
IC 1N2 3C1 3C2 3C3 0.000 0.0 180.0 0.0 0.000
END
******** End of rtf ***********
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Gus Mercier, Jr
NIH - LDRR
gmercier -8 at 8- helix.nih.gov
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Every attempt to employ mathematical
methods in the study of chemical questions
must be considered profoundly irrational
and contrary to the spirit of chemistry ...
If mathematical analysis should ever hold
a prominent place in chemistry -- an aberration
which is happily almost impossible -- it
would occasion a rapid and widespread
degeneration of that science.
Auguste Comte
Philosophie Positive, Paris, 1838
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The underlying physical laws necessary
for the mathematical theory of a large part
of physics and the whole of chemistry are
thus completely known, and the difficulty is
only that the exact application of these laws
leads to equations much too complicated to be soluble.
Dirac, Proc. Roy. Soc (London) 123:714 (1929)
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