Subject: dendrimer builder

From: [email-masked] (Gustavo A. Mercier, Jr.)
Date: Mon, 20 May 1996 16:32:12 -0500

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 = @Ng + 1
LET sto2 = @Nb ** @sto1
LET sto2 = @sto2 - 1
LET sto1 = @Nb - 1
LET NRb = @sto2 / @sto1

LABEL L_CORE

READ SEQU AMT @NRb
GENE @iNc SETUP

! patch the branch
  LABEL L_GEN

!   CALC Zp ( @Nb ) ** ( ( @iNg ) - 1 )
    LET Zp = @iNg - 1
    LET Zp = @Nb ** @Zp

!   CALC Of2 ( @Zp - 1 ) / ( @Nb - 1 )
    LET  sto1 = @Zp - 1
    LET  sto2 = @Nb - 1
    DIVI sto1 BY @sto2      ! This is done to avoid some bug with LET
    SET Of2 @sto1

!   CALC Of1 ( ( ( @Nb ) * ( @Zp ) ) - 1 ) / ( @Nb - 1 )
    LET sto1 = @Nb * @Zp
    LET sto1 = @sto1 - 1
    LET sto2 = @Nb - 1
    LET Of1 = @sto1 / @sto2

    LABEL L_BRANP
!     CALC iRh   @Of2 + @iNb
      LET iRh = @Of2 + @iNb

!     CALC iRt1  @Of1 + 1
      LET iRt1 = @Of1 + 1

!     CALC iRt2  @Of1 + 2
      LET iRt2 = @Of1 + 2

      PATCH DEND @iNc @iRh  @iNc @iRt1   @iNc  @iRt2 SETUP
      SET Of1 @iRt2
      INCR iNb BY 1
      IF @iNb GT @Zp THEN GOTO E_BRANP
      GOTO L_BRANP
    LABEL E_BRANP
    SET iNb 1   ! reset the counter
    INCR iNg BY 1
    IF @iNg GT @Ng THEN GOTO E_GEN
    GOTO L_GEN
  LABEL E_GEN
  SET iNg 1
  INCR iNc BY 1
  IF @iNc GT @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 ***********

****************************************
Gus Mercier, Jr
NIH - LDRR
[email-masked]
****************************************
****************************************
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
-------------------------------------------------------------

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)
-------------------------------------------------------------