Hello All,
I first would like to say this mailing list has helped me tremendously with the AMBER software and components.
Now, I currently have a half lithium battery cell with components:
Propylene Carbonate
Ethylene Carbonate
Graphitic Sheets
Lithium ions
PF6-
I went about trying to build the parameter and co-ordinate files for this configuration as follows
$AMBERHOME/bin/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
source leaprc.gaff
----- Source: /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> loadoff PCA.lib
Loading library: ./PCA.lib
> loadoff PCB.lib
Loading library: ./PCB.lib
> loadoff ECA.lib
Loading library: ./ECA.lib
> loadoff GRA.lib
Loading library: ./GRA.lib
> loadoff PF6.lib
Loading library: ./PF6.lib
> min_rep=loadpdb min_rep.pdb
Loading PDB file: ./min_rep.pdb
Warning: name change in pdb file residue 75 ;
this residue is split into PCB and PCA.
Warning: name change in pdb file residue 79 ;
this residue is split into PCB and PCA.
2 residues had naming warnings.
There are split residues;
residue sequence numbers will not correspond to those in the pdb.
Created a new atom named: H31 within residue: .R<GRA 1>
Created a new atom named: H32 within residue: .R<GRA 1>
Created a new atom named: C160 within residue: .R<GRA 1>
Created a new atom named: H33 within residue: .R<GRA 1>
Created a new atom named: C154 within residue: .R<GRA 1>
Created a new atom named: C155 within residue: .R<GRA 1>
Created a new atom named: C156 within residue: .R<GRA 1>
Created a new atom named: C157 within residue: .R<GRA 1>
Created a new atom named: C158 within residue: .R<GRA 1>
Created a new atom named: C159 within residue: .R<GRA 1>
Added missing heavy atom: .R<GRA 1>.A<CC13 111>
Added missing heavy atom: .R<GRA 1>.A<CC10 115>
Added missing heavy atom: .R<GRA 1>.A<CC12 90>
Added missing heavy atom: .R<GRA 1>.A<CC11 91>
Added missing heavy atom: .R<GRA 1>.A<CC15 70>
Added missing heavy atom: .R<GRA 1>.A<CC14 29>
Added missing heavy atom: .R<GRA 1>.A<CC16 27>
Created a new atom named: H31 within residue: .R<GRA 2>
Created a new atom named: H32 within residue: .R<GRA 2>
Created a new atom named: C160 within residue: .R<GRA 2>
Created a new atom named: H33 within residue: .R<GRA 2>
Created a new atom named: C154 within residue: .R<GRA 2>
Created a new atom named: C155 within residue: .R<GRA 2>
Created a new atom named: C156 within residue: .R<GRA 2>
Created a new atom named: C157 within residue: .R<GRA 2>
Created a new atom named: C158 within residue: .R<GRA 2>
Created a new atom named: C159 within residue: .R<GRA 2>
Added missing heavy atom: .R<GRA 2>.A<CC13 111>
Added missing heavy atom: .R<GRA 2>.A<CC10 115>
Added missing heavy atom: .R<GRA 2>.A<CC12 90>
Added missing heavy atom: .R<GRA 2>.A<CC11 91>
Added missing heavy atom: .R<GRA 2>.A<CC15 70>
Added missing heavy atom: .R<GRA 2>.A<CC14 29>
Added missing heavy atom: .R<GRA 2>.A<CC16 27>
Created a new atom named: H31 within residue: .R<GRA 3>
Created a new atom named: H32 within residue: .R<GRA 3>
Created a new atom named: C160 within residue: .R<GRA 3>
Created a new atom named: H33 within residue: .R<GRA 3>
Created a new atom named: C154 within residue: .R<GRA 3>
Created a new atom named: C155 within residue: .R<GRA 3>
Created a new atom named: C156 within residue: .R<GRA 3>
Created a new atom named: C157 within residue: .R<GRA 3>
Created a new atom named: C158 within residue: .R<GRA 3>
Created a new atom named: C159 within residue: .R<GRA 3>
Added missing heavy atom: .R<GRA 3>.A<CC13 111>
Added missing heavy atom: .R<GRA 3>.A<CC10 115>
Added missing heavy atom: .R<GRA 3>.A<CC12 90>
Added missing heavy atom: .R<GRA 3>.A<CC11 91>
Added missing heavy atom: .R<GRA 3>.A<CC15 70>
Added missing heavy atom: .R<GRA 3>.A<CC14 29>
Added missing heavy atom: .R<GRA 3>.A<CC16 27>
Created a new atom named: H31 within residue: .R<GRA 4>
Created a new atom named: H32 within residue: .R<GRA 4>
Created a new atom named: C160 within residue: .R<GRA 4>
Created a new atom named: H33 within residue: .R<GRA 4>
Created a new atom named: C
154 within residue: .R<GRA 4>
Created a new atom named: C155 within residue: .R<GRA 4>
Created a new atom named: C156 within residue: .R<GRA 4>
Created a new atom named: C157 within residue: .R<GRA 4>
Created a new atom named: C158 within residue: .R<GRA 4>
Created a new atom named: C159 within residue: .R<GRA 4>
Added missing heavy atom: .R<GRA 4>.A<CC13 111>
Added missing heavy atom: .R<GRA 4>.A<CC10 115>
Added missing heavy atom: .R<GRA 4>.A<CC12 90>
Added missing heavy atom: .R<GRA 4>.A<CC11 91>
Added missing heavy atom: .R<GRA 4>.A<CC15 70>
Added missing heavy atom: .R<GRA 4>.A<CC14 29>
Added missing heavy atom: .R<GRA 4>.A<CC16 27>
Added missing heavy atom: .R<PCB 5>.A<C4 9>
Added missing heavy atom: .R<PCB 7>.A<C4 9>
Added missing heavy atom: .R<PCB 9>.A<C4 9>
Added missing heavy atom: .R<PCB 11>.A<C4 9>
Added missing heavy atom: .R<PCB 13>.A<C4 9>
Added missing heavy atom: .R<PCB 15>.A<C4 9>
Added missing heavy atom: .R<PCB 17>.A<C4 9>
Added missing heavy atom: .R<PCB 19>.A<C4 9>
Added missing heavy atom: .R<PCB 21>.A<C4 9>
Added missing heavy atom: .R<PCB 23>.A<C4 9>
Added missing heavy atom: .R<PCB 25>.A<C4 9>
Added missing heavy atom: .R<PCB 27>.A<C4 9>
Added missing heavy atom: .R<PCB 69>.A<C4 9>
Added missing heavy atom: .R<PCB 71>.A<C4 9>
Added missing heavy atom: .R<PCB 73>.A<C4 9>
Added missing heavy atom: .R<PCB 75>.A<O3 2>
Added missing heavy atom: .R<PCB 75>.A<C4 9>
Added missing heavy atom: .R<PCA 76>.A<C1 4>
Added missing heavy atom: .R<PCA 76>.A<C2 3>
Added missing heavy atom: .R<PCA 76>.A<O2 1>
Added missing heavy atom: .R<PCA 76>.A<O1 8>
Added missing heavy atom: .R<PCA 76>.A<C4 10>
Added missing heavy atom: .R<PCA 76>.A<C3 5>
Added missing heavy atom: .R<PCB 78>.A<C4 9>
Added missing heavy atom: .R<PCB 80>.A<C2 3>
Added missing heavy atom: .R<PCB 80>.A<O3 2>
Added missing heavy atom: .R<PCB 80>.A<C4 9>
Added missing heavy atom: .R<PCA 81>.A<C4 10>
Added missing heavy atom: .R<PCA 81>.A<C3 5>
Added missing heavy atom: .R<PCA 81>.A<O2 1>
Added missing heavy atom: .R<PCA 81>.A<C1 4>
Added missing heavy atom: .R<PCA 81>.A<O1 8>
Added missing heavy atom: .R<PCB 83>.A<C4 9>
Added missing heavy atom: .R<PCB 85>.A<C4 9>
Added missing heavy atom: .R<PCB 87>.A<C4 9>
Added missing heavy atom: .R<PCB 89>.A<C4 9>
Added missing heavy atom: .R<PCB 91>.A<C4 9>
Added missing heavy atom: .R<PCB 93>.A<C4 9>
Added missing heavy atom: .R<PCB 161>.A<C4 9>
Added missing heavy atom: .R<PCB 163>.A<C4 9>
Added missing heavy atom: .R<PCB 165>.A<C4 9>
Added missing heavy atom: .R<PCB 167>.A<C4 9>
Added missing heavy atom: .R<PCB 169>.A<C4 9>
Added missing heavy atom: .R<PCB 171>.A<C4 9>
Added missing heavy atom: .R<PCB 173>.A<C4 9>
Added missing heavy atom: .R<PCB 175>.A<C4 9>
Added missing heavy atom: .R<PCB 177>.A<C4 9>
Added missing heavy atom: .R<PCB 179>.A<C4 9>
Leap added 236 missing atoms according to residue templates:
76 Heavy
160 H / lone pairs
The file contained 40 atoms not in residue templates
Then this next, I employed to the 'saveamberparm' command. Up to this point everything is going as expected. After such I was prompted with 'WARNING's.
> saveamberparm min_rep min_rep.prmtop min_rep.inpcrd
Checking Unit.
WARNING: There is a bond of 21.213601 angstroms between:
------- .R<GRA 1>.A<C135 195> and .R<GRA 1>.A<H23 196>
WARNING: There is a bond of 6.082944 angstroms between:
------- .R<GRA 1>.A<C108 193> and .R<GRA 1>.A<C135 195>
WARNING: There is a bond of 16.943482 angstroms between:
------- .R<GRA 1>.A<C108 193> and .R<GRA 1>.A<H22 194>
WARNING: There is a bond of 9.542731 angstroms between:
------- .R<GRA 1>.A<C106 189> and .R<GRA 1>.A<H10 191>
WARNING: There is a bond of 8.943904 angstroms between:
------- .R<GRA 1>.A<C106 189> and .R<GRA 1>.A<H9 190>
WARNING: There is a bond of 4.638284 angstroms between:
------- .R<GRA 1>.A<C144 186> and .R<GRA 1>.A<H8 187>
WARNING: There is a bond of 5.055866 angstroms between:
------- .R<GRA 1>.A<C144 186> and .R<GRA 1>.A<C105 188>
WARNING: There is a bond of 3.804106 angstroms between:
------- .R<GRA 1>.A<C142 184> and .R<GRA 1>.A<C143 185>
WARNING: There is a bond of 15.146066 angstroms between:
------- .R<GRA 1>.A<C153 182> and .R<GRA 1>.A<C104 183>
WARNING: There is a bond of 19.215470 angstroms between:
------- .R<GRA 1>.A<C152 181> and .R<GRA 1>.A<C135 195>
WARNING: There is a bond of 16.937478 angstroms between:
------- .R<GRA 1>.A<C134 178> and .R<GRA 1>.A<C151 180>
WARNING: There is a bond of 9.143248 angstroms between:
------- .R<GRA 1>.A<C79 176> and .R<GRA 1>.A<C134 178>
WARNING: There is a bond of 7.268525 angstroms between:
------- .R<GRA 1>.A<C133 173> and .R<GRA 1>.A<C75 174>
WARNING: There is a bond of 17.844931 angstroms between:
------- .R<GRA 1>.A<C133 173> and .R<GRA 1>.A<C151 180>
WARNING: There is a bond of 17.461010 angstroms between:
------- .R<GRA 1>.A<C150 172> and .R<GRA 1>.A<C133 173>
WARNING: There is a bond of 4.810041 angstroms between:
------- .R<GRA 1>.A<C149 171> and .R<GRA 1>.A<C153 182>
WARNING: There is a bond of 20.752779 angstroms between:
------- .R<GRA 1>.A<C141 169> and .R<GRA 1>.A<C148 170>
WARNING: There is a bond of 4.293915 angstroms between:
------- .R<GRA 1>.A<C138 165> and .R<GRA 1>.A<C140 168>
WARNING: There is a bond of 3.759909 angstroms between:
------- .R<GRA 1>.A<C138 165> and .R<GRA 1>.A<C139 166>
WARNING: There is a bond of 4.813114 angstroms between:
------- .R<GRA 1>.A<C137 163> and .R<GRA 1>.A<H6 164>
WARNING: There is a bond of 8.489174 angstroms between:
------- .R<GRA 1>.A<C126 162> and .R<GRA 1>.A<C137 163>
WARNING: There is a bond of 7.372400 angstroms between:
------- .R<GRA 1>.A<C136 160> and .R<GRA 1>.A<C125 161>
WARNING: There is a bond of 5.037123 angstroms between:
------- .R<GRA 1>.A<C99 159> and .R<GRA 1>.A<C136 160>
WARNING: There is a bond of 17.015535 angstroms between:
------- .R<GRA 1>.A<C147 158> and .R<GRA 1>.A<C99 159>
WARNING: There is a bond of 4.812390 angstroms between:
------- .R<GRA 1>.A<C145 156> and .R<GRA 1>.A<C150 172>
WARNING: There is a bond of 15.147202 angstroms between:
------- .R<GRA 1>.A<C71 155> and .R<GRA 1>.A<C145 156>
WARNING: There is a bond of 22.964772 angstroms between:
------- .R<GRA 1>.A<C117 137> and .R<GRA 1>.A<H18 138>
WARNING: There is a bond of 22.445237 angstroms between:
------- .R<GRA 1>.A<C117 137> and .R<GRA 1>.A<H19 139>
WARNING: There is a bond of 19.892039 angstroms between:
------- .R<GRA 1>.A<C116 131> and .R<GRA 1>.A<C47 132>
WARNING: There is a bond of 22.927334 angstroms between:
------- .R<GRA 1>.A<C115 130> and .R<GRA 1>.A<H20 140>
WARNING: There is a bond of 21.264165 angstroms between:
------- .R<GRA 1>.A<C114 129> and .R<GRA 1>.A<C45 141>
WARNING: There is a bond of 21.629098 angstroms between:
------- .R<GRA 1>.A<C113 127> and .R<GRA 1>.A<H21 128>
WARNING: There is a bond of 17.488380 angstroms between:
------- .R<GRA 1>.A<C112 126> and .R<GRA 1>.A<C113 127>
WARNING: There is a bond of 12.125954 angstroms between:
------- .R<GRA 1>.A<C43 125> and .R<GRA 1>.A<C112 126>
WARNING: There is a bond of 14.450506 angstroms between:
------- .R<GRA 1>.A<CC10 115> and .R<GRA 1>.A<C67 116>
WARNING: There is a bond of 15.225563 angstroms between:
------- .R<GRA 1>.A<C97 114> and .R<GRA 1>.A<CC10 115>
WARNING: There is a bond of 3.702614 angstroms between:
------- .R<GRA 1>.A<CC13 111> and .R<GRA 1>.A<C95 112>
WARNING: There is a bond of 0.015806 angstroms between:
------- .R<GRA 1>.A<C124 110> and .R<GRA 1>.A<CC13 111>
WARNING: There is a bond of 10.930361 angstroms between:
------- .R<GRA 1>.A<C132 99> and .R<GRA 1>.A<H2 100>
WARNING: There is a bond of 12.021857 angstroms between:
------- .R<GRA 1>.A<C132 99> and .R<GRA 1>.A<C118 101>
WARNING: There is a bond of 11.729260 angstroms between:
------- .R<GRA 1>.A<C131 97> and .R<GRA 1>.A<H1 98>
WARNING: There is a bond of 9.443807 angstroms between:
------- .R<GRA 1>.A<C130 95> and .R<GRA 1>.A<H35 96>
WARNING: There is a bond of 3.693813 angstroms between:
------- .R<GRA 1>.A<C130 95> and .R<GRA 1>.A<C131 97>
WARNING: There is a bond of 9.615131 angstroms between:
------- .R<GRA 1>.A<C128 93> and .R<GRA 1>.A<C118 101>
WARNING: There is a bond of 7.221462 angstroms between:
------- .R<GRA 1>.A<CC11 91> and .R<GRA 1>.A<C127 92>
WARNING: There is a bond of 6.787446 angstroms between:
------- .R<GRA 1>.A<CC12 90> and .R<GRA 1>.A<CC11 91>
WARNING: There is a bond of 12.134905 angstroms between:
------- .R<GRA 1>.A<C110 73> and .R<GRA 1>.A<C41 76>
WARNING: There is a bond of 3.737025 angstroms between:
------- .R<GRA 1>.A<C110 73> and .R<GRA 1>.A<C111 74>
WARNING: There is a bond of 15.169884 angstroms between:
------- .R<GRA 1>.A<C39 69> and .R<GRA 1>.A<CC15 70>
WARNING: There is a bond of 6.394891 angstroms between:
------- .R<GRA 1>.A<C87 56> and .R<GRA 1>.A<C127 92>
WARNING: There is a bond of 8.728950 angstroms between:
------- .R<GRA 1>.A<C84 54> and .R<GRA 1>.A<C129 94>
WARNING: There is a bond of 19.208222 angstroms between:
------- .R<GRA 1>.A<C82 50> and .R<GRA 1>.A<H12 51>
WARNING: There is a bond of 18.004444 angstroms between:
------- .R<GRA 1>.A<C103 35> and .R<GRA 1>.A<H24 36>
WARNING: There is a bond of 5.578938 angstroms between:
------- .R<GRA 1>.A<C103 35> and .R<GRA 1>.A<CC15 70>
WARNING: There is a bond of 12.114517 angstroms between:
------- .R<GRA 1>.A<C102 34> and .R<GRA 1>.A<C37 37>
WARNING: There is a bond of 3.711847 angstroms between:
------- .R<GRA 1>.A<C102 34> and .R<GRA 1>.A<C103 35>
WARNING: There is a bond of 16.684730 angstroms between:
------- .R<GRA 1>.A<C101 32> and .R<GRA 1>.A<H25 33>
WARNING: There is a bond of 19.103766 angstroms between:
------- .R<GRA 1>.A<CC14 29> and .R<GRA 1>.A<H26 30>
WARNING: There is a bond of 18.057440 angstroms between:
------- .R<GRA 1>.A<CC16 27> and .R<GRA 1>.A<H27 28>
WARNING: There is a bond of 15.956869 angstroms between:
------- .R<GRA 1>.A<C34 25> and .R<GRA 1>.A<CC16 27>
WARNING: There is a bond of 15.917710 angstroms between:
------- .R<GRA 1>.A<C35 23> and .R<GRA 1>.A<C100 31>
WARNING: There is a bond of 20.303583 angstroms between:
------- .R<GRA 1>.A<C51 12> and .R<GRA 1>.A<H11 13>
WARNING: There is a bond of 21.209235 angstroms between:
------- .R<GRA 2>.A<C135 195> and .R<GRA 2>.A<H23 196>
WARNING: There is a bond of 6.081791 angstroms between:
------- .R<GRA 2>.A<C108 193> and .R<GRA 2>.A<C135 195>
WARNING: There is a bond of 16.943160 angstroms between:
------- .R<GRA 2>.A<C108 193> and .R<GRA 2>.A<H22 194>
WARNING: There is a bond of 9.535005 angstroms between:
------- .R<GRA 2>.A<C106 189> and .R<GRA 2>.A<H10 191>
WARNING: There is a bond of 8.944448 angstroms between:
------- .R<GRA 2>.A<C106 189> and .R<GRA 2>.A<H9 190>
WARNING: There is a bond of 4.636749 angstroms between:
------- .R<GRA 2>.A<C144 186> and .R<GRA 2>.A<H8 187>
WARNING: There is a bond of 5.057252 angstroms between:
------- .R<GRA 2>.A<C144 186> and .R<GRA 2>.A<C105 188>
WARNING: There is a bond of 3.805923 angstroms between:
------- .R<GRA 2>.A<C142 184> and .R<GRA 2>.A<C143 185>
WARNING: There is a bond of 15.145921 angstroms between:
------- .R<GRA 2>.A<C153 182> and .R<GRA 2>.A<C104 183>
WARNING: There is a bond of 19.212355 angstroms between:
------- .R<GRA 2>.A<C152 181> and .R<GRA 2>.A<C135 195>
WARNING: There is a bond of 16.940585 angstroms between:
------- .R<GRA 2>.A<C134 178> and .R<GRA 2>.A<C151 180>
WARNING: There is a bond of 9.146177 angstroms between:
------- .R<GRA 2>.A<C79 176> and .R<GRA 2>.A<C134 178>
WARNING: There is a bond of 7.267551 angstroms between:
------- .R<GRA 2>.A<C133 173> and .R<GRA 2>.A<C75 174>
WARNING: There is a bond of 17.842227 angstroms between:
------- .R<GRA 2>.A<C133 173> and .R<GRA 2>.A<C151 180>
WARNING: There is a bond of 17.454967 angstroms between:
------- .R<GRA 2>.A<C150 172> and .R<GRA 2>.A<C133 173>
WARNING: There is a bond of 4.805023 angstroms between:
------- .R<GRA 2>.A<C149 171> and .R<GRA 2>.A<C153 182>
WARNING: There is a bond of 20.746491 angstroms between:
------- .R<GRA 2>.A<C141 169> and .R<GRA 2>.A<C148 170>
WARNING: There is a bond of 4.291778 angstroms between:
------- .R<GRA 2>.A<C138 165> and .R<GRA 2>.A<C140 168>
WARNING: There is a bond of 3.757408 angstroms between:
------- .R<GRA 2>.A<C138 165> and .R<GRA 2>.A<C139 166>
WARNING: There is a bond of 4.812271 angstroms between:
------- .R<GRA 2>.A<C137 163> and .R<GRA 2>.A<H6 164>
WARNING: There is a bond of 8.492348 angstroms between:
------- .R<GRA 2>.A<C126 162> and .R<GRA 2>.A<C137 163>
WARNING: There is a bond of 7.370856 angstroms between:
------- .R<GRA 2>.A<C136 160> and .R<GRA 2>.A<C125 161>
WARNING: There is a bond of 5.039192 angstroms between:
------- .R<GRA 2>.A<C99 159> and .R<GRA 2>.A<C136 160>
WARNING: There is a bond of 17.010701 angstroms between:
------- .R<GRA 2>.A<C147 158> and .R<GRA 2>.A<C99 159>
WARNING: There is a bond of 4.808363 angstroms between:
------- .R<GRA 2>.A<C145 156> and .R<GRA 2>.A<C150 172>
WARNING: There is a bond of 15.139334 angstroms between:
------- .R<GRA 2>.A<C71 155> and .R<GRA 2>.A<C145 156>
WARNING: There is a bond of 22.959229 angstroms between:
------- .R<GRA 2>.A<C117 137> and .R<GRA 2>.A<H18 138>
WARNING: There is a bond of 22.440423 angstroms between:
------- .R<GRA 2>.A<C117 137> and .R<GRA 2>.A<H19 139>
WARNING: There is a bond of 19.891742 angstroms between:
------- .R<GRA 2>.A<C116 131> and .R<GRA 2>.A<C47 132>
WARNING: There is a bond of 22.921682 angstroms between:
------- .R<GRA 2>.A<C115 130> and .R<GRA 2>.A<H20 140>
WARNING: There is a bond of 21.258602 angstroms between:
------- .R<GRA 2>.A<C114 129> and .R<GRA 2>.A<C45 141>
WARNING: There is a bond of 21.626657 angstroms between:
------- .R<GRA 2>.A<C113 127> and .R<GRA 2>.A<H21 128>
WARNING: There is a bond of 17.480059 angstroms between:
------- .R<GRA 2>.A<C112 126> and .R<GRA 2>.A<C113 127>
WARNING: There is a bond of 12.126403 angstroms between:
------- .R<GRA 2>.A<C43 125> and .R<GRA 2>.A<C112 126>
WARNING: There is a bond of 14.444729 angstroms between:
------- .R<GRA 2>.A<CC10 115> and .R<GRA 2>.A<C67 116>
WARNING: There is a bond of 15.215866 angstroms between:
------- .R<GRA 2>.A<C97 114> and .R<GRA 2>.A<CC10 115>
WARNING: There is a bond of 3.703157 angstroms between:
------- .R<GRA 2>.A<CC13 111> and .R<GRA 2>.A<C95 112>
After such warnings I was prompted with these FATAL ERRORS:
FATAL: Atom .R<GRA 1>.A<H31 197> does not have a type.
FATAL: Atom .R<GRA 1>.A<H32 198> does not have a type.
FATAL: Atom .R<GRA 1>.A<C160 199> does not have a type.
FATAL: Atom .R<GRA 1>.A<H33 200> does not have a type.
FATAL: Atom .R<GRA 1>.A<C154 201> does not have a type.
FATAL: Atom .R<GRA 1>.A<C155 202> does not have a type.
FATAL: Atom .R<GRA 1>.A<C156 203> does not have a type.
FATAL: Atom .R<GRA 1>.A<C157 204> does not have a type.
FATAL: Atom .R<GRA 1>.A<C158 205> does not have a type.
FATAL: Atom .R<GRA 1>.A<C159 206> does not have a type.
FATAL: Atom .R<GRA 2>.A<H31 197> does not have a type.
FATAL: Atom .R<GRA 2>.A<H32 198> does not have a type.
FATAL: Atom .R<GRA 2>.A<C160 199> does not have a type.
FATAL: Atom .R<GRA 2>.A<H33 200> does not have a type.
FATAL: Atom .R<GRA 2>.A<C154 201> does not have a type.
FATAL: Atom .R<GRA 2>.A<C155 202> does not have a type.
FATAL: Atom .R<GRA 2>.A<C156 203> does not have a type.
FATAL: Atom .R<GRA 2>.A<C157 204> does not have a type.
FATAL: Atom .R<GRA 2>.A<C158 205> does not have a type.
FATAL: Atom .R<GRA 2>.A<C159 206> does not have a type.
FATAL: Atom .R<GRA 3>.A<H31 197> does not have a type.
FATAL: Atom .R<GRA 3>.A<H32 198> does not have a type.
FATAL: Atom .R<GRA 3>.A<C160 199> does not have a type.
FATAL: Atom .R<GRA 3>.A<H33 200> does not have a type.
FATAL: Atom .R<GRA 3>.A<C154 201> does not have a type.
FATAL: Atom .R<GRA 3>.A<C155 202> does not have a type.
FATAL: Atom .R<GRA 3>.A<C156 203> does not have a type.
FATAL: Atom .R<GRA 3>.A<C157 204> does not have a type.
FATAL: Atom .R<GRA 3>.A<C158 205> does not have a type.
FATAL: Atom .R<GRA 3>.A<C159 206> does not have a type.
FATAL: Atom .R<GRA 4>.A<H31 197> does not have a type.
FATAL: Atom .R<GRA 4>.A<H32 198> does not have a type.
FATAL: Atom .R<GRA 4>.A<C160 199> does not have a type.
FATAL: Atom .R<GRA 4>.A<H33 200> does not have a type.
FATAL: Atom .R<GRA 4>.A<C154 201> does not have a type.
FATAL: Atom .R<GRA 4>.A<C155 202> does not have a type.
FATAL: Atom .R<GRA 4>.A<C156 203> does not have a type.
FATAL: Atom .R<GRA 4>.A<C157 204> does not have a type.
FATAL: Atom .R<GRA 4>.A<C158 205> does not have a type.
FATAL: Atom .R<GRA 4>.A<C159 206> does not have a type.
Failed to generate parameters
Parameter file was not saved.
>From the 'WARNING's and the 'FATAL ERROR's narrow the problem down to the Graphitic Sheets. There is obviously a problem but I am unable to pin point exactly what. I created a .lib file for the Graphitic Sheets including the parameters needed. The following is the contents of this file, GRA.lib. I would appreciate some help on this issue.
Thank You
Shalton Evans
Raptor-login[10] shalton$ cat GRA.lib
!!index array str
"GRA"
!entry.GRA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"C1" "ca" 0 1 131072 1 6 -0.012500
"H30" "ha" 0 1 131072 2 1 0.0
"C2" "ca" 0 1 131072 3 6 -0.012500
"H29" "ha" 0 1 131072 4 1 0.0
"C3" "ca" 0 1 131072 5 6 -0.012500
"C4" "ca" 0 1 131072 6 6 -0.012500
"C5" "ca" 0 1 131072 7 6 -0.012500
"C6" "ca" 0 1 131072 8 6 -0.012500
"C49" "ca" 0 1 131072 9 6 -0.012500
"C50" "ca" 0 1 131072 10 6 -0.012500
"HH3" "ha" 0 1 131072 11 1 0.0
"C51" "ca" 0 1 131072 12 6 -0.012500
"H11" "ha" 0 1 131072 13 1 0.0
"C52" "ca" 0 1 131072 14 6 -0.012500
"C53" "ca" 0 1 131072 15 6 -0.012500
"C54" "ca" 0 1 131072 16 6 -0.012500
"C58" "ca" 0 1 131072 17 6 -0.012500
"C10" "ca" 0 1 131072 18 6 -0.012500
"C9" "ca" 0 1 131072 19 6 -0.012500
"C8" "ca" 0 1 131072 20 6 -0.012500
"C7" "ca" 0 1 131072 21 6 -0.012500
"C36" "ca" 0 1 131072 22 6 -0.012500
"C35" "ca" 0 1 131072 23 6 -0.012500
"C33" "ca" 0 1 131072 24 6 -0.012500
"C34" "ca" 0 1 131072 25 6 -0.012500
"H28" "ha" 0 1 131072 26 1 0.0
"CC16" "ca" 0 1 131072 27 6 -0.012500
"H27" "ha" 0 1 131072 28 1 0.0
"CC14" "ca" 0 1 131072 29 6 -0.012500
"H26" "ha" 0 1 131072 30 1 0.0
"C100" "ca" 0 1 131072 31 6 -0.012500
"C101" "ca" 0 1 131072 32 6 -0.012500
"H25" "ha" 0 1 131072 33 1 0.0
"C102" "ca" 0 1 131072 34 6 -0.012500
"C103" "ca" 0 1 131072 35 6 -0.012500
"H24" "ha" 0 1 131072 36 1 0.0
"C37" "ca" 0 1 131072 37 6 -0.012500
"C38" "ca" 0 1 131072 38 6 -0.012500
"C11" "ca" 0 1 131072 39 6 -0.012500
"C12" "ca" 0 1 131072 40 6 -0.012500
"C13" "ca" 0 1 131072 41 6 -0.012500
"C14" "ca" 0 1 131072 42 6 -0.012500
"C62" "ca" 0 1 131072 43 6 -0.012500
"C57" "ca" 0 1 131072 44 6 -0.012500
"C56" "ca" 0 1 131072 45 6 -0.012500
"C55" "ca" 0 1 131072 46 6 -0.012500
"C90" "ca" 0 1 131072 47 6 -0.012500
"C86" "ca" 0 1 131072 48 6 -0.012500
"C81" "ca" 0 1 131072 49 6 -0.012500
"C82" "ca" 0 1 131072 50 6 -0.012500
"H12" "ha" 0 1 131072 51 1 0.0
"C83" "ca" 0 1 131072 52 6 -0.012500
"H34" "ha" 0 1 131072 53 1 0.0
"C84" "ca" 0 1 131072 54 6 -0.012500
"C85" "ca" 0 1 131072 55 6 -0.012500
"C87" "ca" 0 1 131072 56 6 -0.012500
"C88" "ca" 0 1 131072 57 6 -0.012500
"C89" "ca" 0 1 131072 58 6 -0.012500
"C94" "ca" 0 1 131072 59 6 -0.012500
"C59" "ca" 0 1 131072 60 6 -0.012500
"C60" "ca" 0 1 131072 61 6 -0.012500
"C61" "ca" 0 1 131072 62 6 -0.012500
"C66" "ca" 0 1 131072 63 6 -0.012500
"C18" "ca" 0 1 131072 64 6 -0.0125
00
"C17" "ca" 0 1 131072 65 6 -0.012500
"C16" "ca" 0 1 131072 66 6 -0.012500
"C15" "ca" 0 1 131072 67 6 -0.012500
"C40" "ca" 0 1 131072 68 6 -0.012500
"C39" "ca" 0 1 131072 69 6 -0.012500
"CC15" "ca" 0 1 131072 70 6 -0.012500
"C109" "ca" 0 1 131072 71 6 -0.012500
"HH2" "ha" 0 1 131072 72 1 0.0
"C110" "ca" 0 1 131072 73 6 -0.012500
"C111" "ca" 0 1 131072 74 6 -0.012500
"H13" "ha" 0 1 131072 75 1 0.0
"C41" "ca" 0 1 131072 76 6 -0.012500
"C42" "ca" 0 1 131072 77 6 -0.012500
"C19" "ca" 0 1 131072 78 6 -0.012500
"C20" "ca" 0 1 131072 79 6 -0.012500
"C21" "ca" 0 1 131072 80 6 -0.012500
"C22" "ca" 0 1 131072 81 6 -0.012500
"C70" "ca" 0 1 131072 82 6 -0.012500
"C65" "ca" 0 1 131072 83 6 -0.012500
"C64" "ca" 0 1 131072 84 6 -0.012500
"C63" "ca" 0 1 131072 85 6 -0.012500
"C98" "ca" 0 1 131072 86 6 -0.012500
"C93" "ca" 0 1 131072 87 6 -0.012500
"C92" "ca" 0 1 131072 88 6 -0.012500
"C91" "ca" 0 1 131072 89 6 -0.012500
"CC12" "ca" 0 1 131072 90 6 -0.012500
"CC11" "ca" 0 1 131072 91 6 -0.012500
"C127" "ca" 0 1 131072 92 6 -0.012500
"C128" "ca" 0 1 131072 93 6 -0.012500
"C129" "ca" 0 1 131072 94 6 -0.012500
"C130" "ca" 0 1 131072 95 6 -0.012500
"H35" "ha" 0 1 131072 96 1 0.0
"C131" "ca" 0 1 131072 97 6 -0.012500
"H1" "ha" 0 1 131072 98 1 0.0
"C132" "ca" 0 1 131072 99 6 -0.012500
"H2" "ha" 0 1 131072 100 1 0.0
"C118" "ca" 0 1 131072 101 6 -0.012500
"C119" "ca" 0 1 131072 102 6 -0.012500
"H3" "ha" 0 1 131072 103 1 0.0
"C120" "ca" 0 1 131072 104 6 -0.012500
"C121" "ca" 0 1 131072 105 6 -0.012500
"H4" "ha" 0 1 131072 106 1 0.0
"C122" "ca" 0 1 131072 107 6 -0.012500
"C123" "ca" 0 1 131072 108 6 -0.012500
"H5" "ha" 0 1 131072 109 1 0.0
"C124" "ca" 0 1 131072 110 6 -0.012500
"CC13" "ca" 0 1 131072 111 6 -0.012500
"C95" "ca" 0 1 131072 112 6 -0.012500
"C96" "ca" 0 1 131072 113 6 -0.012500
"C97" "ca" 0 1 131072 114 6 -0.012500
"CC10" "ca" 0 1 131072 115 6 -0.012500
"C67" "ca" 0 1 131072 116 6 -0.012500
"C68" "ca" 0 1 131072 117 6 -0.012500
"C69" "ca" 0 1 131072 118 6 -0.012500
"C74" "ca" 0 1 131072 119 6 -0.012500
"C26" "ca" 0 1 131072 120 6 -0.012500
"C25" "ca" 0 1 131072 121 6 -0.012500
"C24" "ca" 0 1 131072 122 6 -0.012500
"C23" "ca" 0 1 131072 123 6 -0.012500
"C44" "ca" 0 1 131072 124 6 -0.012500
"C43" "ca" 0 1 131072 125 6 -0.012500
"C112" "ca" 0 1 131072 126 6 -0.012500
"C113" "ca" 0 1 131072 127 6 -0.012500
"H21" "ha" 0 1 131072 128 1 0.0
"C114" "ca" 0 1 131072 129 6 -0.012500
"C115" "cc" 0 1 131072 130 6 -0.012500
"C116" "cc" 0 1 131072 131 6 -0.012500
"C47" "ca" 0 1 131072 132 6 -0.012500
"C48" "ca" 0 1 131072 133 6 -0.012500
"C31" "ca" 0 1 131072 134 6 -0.012500
"H16" "ha" 0 1 131072 135 1 0.0
"H17" "ha" 0 1 131072 136 1 0.0
"C117" "c2" 0 1 131072 137 6 -0.012500
"H18" "ha" 0 1 131072 138 1 0.0
"H19" "ha" 0 1 131072 139 1 0.0
"H20" "ha" 0 1 131072 140 1 0.0
"C45" "ca" 0 1 131072 141 6 -0.012500
"C46" "ca" 0 1 131072 142 6 -0.012500
"C27" "ca" 0 1 131072 143 6 -0.012500
"C28" "ca" 0 1 131072 144 6 -0.012500
"C29" "ca" 0 1 131072 145 6 -0.012500
"C32" "ca" 0 1 131072 146 6 -0.012500
"C80" "ca" 0 1 131072 147 6 -0.012500
"C77" "ca" 0 1 131072 148 6 -0.012500
"H14" "ha" 0 1 131072 149 1 0.0
"H15" "ha" 0 1 131072 150 1 0.0
"C30" "ca" 0 1 131072 151 6 -0.012500
"C78" "ca" 0 1 131072 152 6 -0.012500
"C73" "ca" 0 1 131072 153 6 -0.012500
"C72" "ca" 0 1 131072 154 6 -0.012500
"C71" "ca" 0 1 131072 155 6 -0.012500
"C145" "ca" 0 1 131072 156 6 -0.012500
"C146" "ca" 0 1 131072 157 6 -0.012500
"C147" "ca" 0 1 131072 158 6 -0.012500
"C99" "ca" 0 1 131072 159 6 -0.012500
"C136" "ca" 0 1 131072 160 6 -0.012500
"C125" "ca" 0 1 131072 161 6 -0.012500
"C126" "ca" 0 1 131072 162 6 -0.012500
"C137" "ca" 0 1 131072 163 6 -0.012500
"H6" "ha" 0 1 131072 164 1 0.0
"C138" "ca" 0 1 131072 165 6 -0.012500
"C139" "ca" 0 1 131072 166 6 -0.012500
"H7" "ha" 0 1 131072 167 1 0.0
"C140" "ca" 0 1 131072 168 6 -0.012500
"C141" "ca" 0 1 131072 169 6 -0.012500
"C148" "ca" 0 1 131072 170 6 -0.012500
"C149" "ca" 0 1 131072 171 6 -0.012500
"C150" "ca" 0 1 131072 172 6 -0.012500
"C133" "ca" 0 1 131072 173 6 -0.012500
"C75" "ca" 0 1 131072 174 6 -0.012500
"C76" "ca" 0 1 131072 175 6 -0.012500
"C79" "ca" 0 1 131072 176 6 -0.012500
"H36" "ha" 0 1 131072 177 1 0.0
"C134" "ca" 0 1 131072 178 6 -0.012500
"HH1" "ha" 0 1 131072 179 1 0.0
"C151" "ca" 0 1 131072 180 6 -0.012500
"C152" "ca" 0 1 131072 181 6 -0.012500
"C153" "ca" 0 1 131072 182 6 -0.012500
"C104" "ca" 0 1 131072 183 6 -0.012500
"C142" "ca" 0 1 131072 184 6 -0.012500
"C143" "ca" 0 1 131072 185 6 -0.012500
"C144" "cc" 0 1 131072 186 6 -0.012500
"H8" "ha" 0 1 131072 187 1 0.0
"C105" "cc" 0 1 131072 188 6 -0.012500
"C106" "c2" 0 1 131072 189 6 -0.012500
"H9" "ha" 0 1 131072 190 1 0.0
"H10" "ha" 0 1 131072 191 1 0.0
"C107" "ca" 0 1 131072 192 6 -0.012500
"C108" "ca" 0 1 131072 193 6 -0.012500
"H22" "ha" 0 1 131072 194 1 0.0
"C135" "ca" 0 1 131072 195 6 -0.012500
"H23" "ha" 0 1 131072 196 1 0.0
!entry.GRA.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"C1" "ca" 0 -1 0.0
"H30" "ha" 0 -1 0.0
"C2" "ca" 0 -1 0.0
"H29" "ha" 0 -1 0.0
"C3" "ca" 0 -1 0.0
"C4" "ca" 0 -1 0.0
"C5" "ca" 0 -1 0.0
"C6" "ca" 0 -1 0.0
"C49" "ca" 0 -1 0.0
"C50" "ca" 0 -1 0.0
"HH3" "ha" 0 -1 0.0
"C51" "ca" 0 -1 0.0
"H11" "ha" 0 -1 0.0
"C52" "ca" 0 -1 0.0
"C53" "ca" 0 -1 0.0
"C54" "ca" 0 -1 0.0
"C58" "ca" 0 -1 0.0
"C10" "ca" 0 -1 0.0
"C9" "ca" 0 -1 0.0
"C8" "ca" 0 -1 0.0
"C7" "ca" 0 -1 0.0
"C36" "ca" 0 -1 0.0
"C35" "ca" 0 -1 0.0
"C33" "ca" 0 -1 0.0
"C34" "ca" 0 -1 0.0
"H28" "ha" 0 -1 0.0
"CC16" "ca" 0 -1 0.0
"H27" "ha" 0 -1 0.0
"CC14" "ca" 0 -1 0.0
"H26" "ha" 0 -1 0.0
"C100" "ca" 0 -1 0.0
"C101" "ca" 0 -1 0.0
"H25" "ha" 0 -1 0.0
"C102" "ca" 0 -1 0.0
"C103" "ca" 0 -1 0.0
"H24" "ha" 0 -1 0.0
"C37" "ca" 0 -1 0.0
"C38" "ca" 0 -1 0.0
"C11" "ca" 0 -1 0.0
"C12" "ca" 0 -1 0.0
"C13" "ca" 0 -1 0.0
"C14" "ca" 0 -1 0.0
"C62" "ca" 0 -1 0.0
"C57" "ca" 0 -1 0.0
"C56" "ca" 0 -1 0.0
"C55" "ca" 0 -1 0.0
"C90" "ca" 0 -1 0.0
"C86" "ca" 0 -1 0.0
"C81" "ca" 0 -1 0.0
"C82" "ca" 0 -1 0.0
"H12" "ha" 0 -1 0.0
"C83" "ca" 0 -1 0.0
"H34" "ha" 0 -1 0.0
"C84" "ca" 0 -1 0.0
"C85" "ca" 0 -1 0.0
"C87" "ca" 0 -1 0.0
"C88" "ca" 0 -1 0.0
"C89" "ca" 0 -1 0.0
"C94" "ca" 0 -1 0.0
"C59" "ca" 0 -1 0.0
"C60" "ca" 0 -1 0.0
"C61" "ca" 0 -1 0.0
"C66" "ca" 0 -1 0.0
"C18" "ca" 0 -1 0.0
"C17" "ca" 0 -1 0.0
"C16" "ca" 0 -1 0.0
"C15" "ca" 0 -1 0.0
"C40" "ca" 0 -1 0.0
"C39" "ca" 0 -1 0.0
"CC15" "ca" 0 -1 0.0
"C109" "ca" 0 -1 0.0
"HH2" "ha" 0 -1 0.0
"C110" "ca" 0 -1 0.0
"C111" "ca" 0 -1 0.0
"H13" "ha" 0 -1 0.0
"C41" "ca" 0 -1 0.0
"C42" "ca" 0 -1 0.0
"C19" "ca" 0 -1 0.0
"C20" "ca" 0 -1 0.0
"C21" "ca" 0 -1 0.0
"C22" "ca" 0 -1 0.0
"C70" "ca" 0 -1 0.0
"C65" "ca" 0 -1 0.0
"C64" "ca" 0 -1 0.0
"C63" "ca" 0 -1 0.0
"C98" "ca" 0 -1 0.0
"C93" "ca" 0 -1 0.0
"C92" "ca" 0 -1 0.0
"C91" "ca" 0 -1 0.0
"CC12" "ca" 0 -1 0.0
"CC11" "ca" 0 -1 0.0
"C127" "ca" 0 -1 0.0
"C128" "ca" 0 -1 0.0
"C129" "ca" 0 -1 0.0
"C130" "ca" 0 -1 0.0
"H35" "ha" 0 -1 0.0
"C131" "ca" 0 -1 0.0
"H1" "ha" 0 -1 0.0
"C132" "ca" 0 -1 0.0
"H2" "ha" 0 -1 0.0
"C118" "ca" 0 -1 0.0
"C119" "ca" 0 -1 0.0
"H3" "ha" 0 -1 0.0
"C120" "ca" 0 -1 0.0
"C121" "ca" 0 -1 0.0
"H4" "ha" 0 -1 0.0
"C122" "ca" 0 -1 0.0
"C123" "ca" 0 -1 0.0
"H5" "ha" 0 -1 0.0
"C124" "ca" 0 -1 0.0
"CC13" "ca" 0 -1 0.0
"C95" "ca" 0 -1 0.0
"C96" "ca" 0 -1 0.0
"C97" "ca" 0 -1 0.0
"CC10" "ca" 0 -1 0.0
"C67" "ca" 0 -1 0.0
"C68" "ca" 0 -1 0.0
"C69" "ca" 0 -1 0.0
"C74" "ca" 0 -1 0.0
"C26" "ca" 0 -1 0.0
"C25" "ca" 0 -1 0.0
"C24" "ca" 0 -1 0.0
"C23" "ca" 0 -1 0.0
"C44" "ca" 0 -1 0.0
"C43" "ca" 0 -1 0.0
"C112" "ca" 0 -1 0.0
"C113" "ca" 0 -1 0.0
"H21" "ha" 0 -1 0.0
"C114" "ca" 0 -1 0.0
"C115" "cc" 0 -1 0.0
"C116" "cc" 0 -1 0.0
"C47" "ca" 0 -1 0.0
"C48" "ca" 0 -1 0.0
"C31" "ca" 0 -1 0.0
"H16" "ha" 0 -1 0.0
"H17" "ha" 0 -1 0.0
"C117" "c2" 0 -1 0.0
"H18" "ha" 0 -1 0.0
"H19" "ha" 0 -1 0.0
"H20" "ha" 0 -1 0.0
"C45" "ca" 0 -1 0.0
"C46" "ca" 0 -1 0.0
"C27" "ca" 0 -1 0.0
"C28" "ca" 0 -1 0.0
"C29" "ca" 0 -1 0.0
"C32" "ca" 0 -1 0.0
"C80" "ca" 0 -1 0.0
"C77" "ca" 0 -1 0.0
"H14" "ha" 0 -1 0.0
"H15" "ha" 0 -1 0.0
"C30" "ca" 0 -1 0.0
"C78" "ca" 0 -1 0.0
"C73" "ca" 0 -1 0.0
"C72" "ca" 0 -1 0.0
"C71" "ca" 0 -1 0.0
"C145" "ca" 0 -1 0.0
"C146" "ca" 0 -1 0.0
"C147" "ca" 0 -1 0.0
"C99" "ca" 0 -1 0.0
"C136" "ca" 0 -1 0.0
"C125" "ca" 0 -1 0.0
"C126" "ca" 0 -1 0.0
"C137" "ca" 0 -1 0.0
"H6" "ha" 0 -1 0.0
"C138" "ca" 0 -1 0.0
"C139" "ca" 0 -1 0.0
"H7" "ha" 0 -1 0.0
"C140" "ca" 0 -1 0.0
"C141" "ca" 0 -1 0.0
"C148" "ca" 0 -1 0.0
"C149" "ca" 0 -1 0.0
"C150" "ca" 0 -1 0.0
"C133" "ca" 0 -1 0.0
"C75" "ca" 0 -1 0.0
"C76" "ca" 0 -1 0.0
"C79" "ca" 0 -1 0.0
"H36" "ha" 0 -1 0.0
"C134" "ca" 0 -1 0.0
"HH1" "ha" 0 -1 0.0
"C151" "ca" 0 -1 0.0
"C152" "ca" 0 -1 0.0
"C153" "ca" 0 -1 0.0
"C104" "ca" 0 -1 0.0
"C142" "ca" 0 -1 0.0
"C143" "ca" 0 -1 0.0
"C144" "cc" 0 -1 0.0
"H8" "ha" 0 -1 0.0
"C105" "cc" 0 -1 0.0
"C106" "c2" 0 -1 0.0
"H9" "ha" 0 -1 0.0
"H10" "ha" 0 -1 0.0
"C107" "ca" 0 -1 0.0
"C108" "ca" 0 -1 0.0
"H22" "ha" 0 -1 0.0
"C135" "ca" 0 -1 0.0
"H23" "ha" 0 -1 0.0
!entry.GRA.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.GRA.unit.childsequence single int
2
!entry.GRA.unit.connect array int
0
0
!entry.GRA.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 3 4
1 8 4
3 4 1
3 5 4
5 24 4
5 6 4
6 7 4
6 21 4
7 8 4
7 18 4
8 9 4
9 10 4
9 16 4
10 11 1
10 12 4
12 13 1
12 14 4
14 49 4
14 15 4
15 16 4
15 46 4
16 17 4
17 18 4
17 44 4
18 19 4
19 20 4
19 42 4
20 21 4
20 39 4
21 22 4
22 23 4
22 37 4
23 24 4
23 31 4
24 25 4
25 26 1
25 27 4
27 28 1
27 29 4
29 30 1
29 31 4
31 32 4
32 33 1
32 34 4
34 37 4
34 35 4
35 36 1
35 70 4
37 38 4
38 39 4
38 69 4
39 40 4
40 41 4
40 67 4
41 42 4
41 64 4
42 43 4
43 44 4
43 62 4
44 45 4
45 46 4
45 60 4
46 47 4
47 48 4
47 58 4
48 49 4
48 55 4
49 50 4
50 51 1
50 52 4
52 53 1
52 54 4
54 94 4
54 55 4
55 56 4
56 92 4
56 57 4
57 58 4
57 89 4
58 59 4
59 60 4
59 87 4
60 61 4
61 62 4
61 85 4
62 63 4
63 64 4
63 83 4
64 65 4
65 66 4
65 81 4
66 67 4
66 78 4
67 68 4
68 69 4
68 76 4
69 70 4
70 71 4
71 72 1
71 73 4
73 76 4
73 74 4
74 75 1
74 126 4
76 77 4
77 78 4
77 125 4
78 79 4
79 80 4
79 123 4
80 81 4
80 120 4
81 82 4
82 83 4
82 118 4
83 84 4
84 85 4
84 116 4
85 86 4
86 87 4
86 114 4
87 88 4
88 89 4
88 112 4
89 90 4
90 91 4
90 110 4
91 92 4
91 104 4
92 93 4
93 94 4
93 101 4
94 95 4
95 96 1
95 97 4
97 98 1
97 99 4
99 100 1
99 101 4
101 102 4
102 103 1
102 104 4
104 105 4
105 106 1
105 107 4
107 110 4
107 108 4
108 109 1
108 162 4
110 111 4
111 112 4
111 161 4
112 113 4
113 114 4
113 159 4
114 115 4
115 116 4
115 157 4
116 117 4
117 118 4
117 155 4
118 119 4
119 120 4
119 153 4
120 121 4
121 122 4
121 151 4
122 123 4
122 143 4
123 124 4
124 125 4
124 141 4
125 126 4
126 127 4
127 128 1
127 129 4
129 141 4
129 130 4
130 140 1
130 131 4
131 132 4
131 137 2
132 142 4
132 133 4
133 134 4
133 136 1
134 144 4
134 135 1
137 138 1
137 139 1
141 142 4
142 143 4
143 144 4
144 145 4
145 151 4
145 146 4
146 147 4
146 150 1
147 148 4
147 149 1
148 152 4
148 175 4
151 152 4
152 153 4
153 154 4
154 155 4
154 174 4
155 156 4
156 157 4
156 172 4
157 158 4
158 159 4
158 170 4
159 160 4
160 161 4
160 168 4
161 162 4
162 163 4
163 164 1
163 165 4
165 168 4
165 166 4
166 167 1
166 185 4
168 169 4
169 170 4
169 184 4
170 171 4
171 172 4
171 182 4
172 173 4
173 174 4
173 180 4
174 175 4
175 176 4
176 178 4
176 177 1
178 180 4
178 179 1
180 181 4
181 182 4
181 195 4
182 183 4
183 184 4
183 192 4
184 185 4
185 186 2
186 187 1
186 188 1
188 192 1
188 189 2
189 191 1
189 190 1
192 193 4
193 195 4
193 194 1
195 196 1
!entry.GRA.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
"R" 1 "A" 17
"R" 1 "A" 18
"R" 1 "A" 19
"R" 1 "A" 20
"R" 1 "A" 21
"R" 1 "A" 22
"R" 1 "A" 23
"R" 1 "A" 24
"R" 1 "A" 25
"R" 1 "A" 26
"R" 1 "A" 27
"R" 1 "A" 28
"R" 1 "A" 29
"R" 1 "A" 30
"R" 1 "A" 31
"R" 1 "A" 32
"R" 1 "A" 33
"R" 1 "A" 34
"R" 1 "A" 35
"R" 1 "A" 36
"R" 1 "A" 37
"R" 1 "A" 38
"R" 1 "A" 39
"R" 1 "A" 40
"R" 1 "A" 41
"R" 1 "A" 42
"R" 1 "A" 43
"R" 1 "A" 44
"R" 1 "A" 45
"R" 1 "A" 46
"R" 1 "A" 47
"R" 1 "A" 48
"R" 1 "A" 49
"R" 1 "A" 50
"R" 1 "A" 51
"R" 1 "A" 52
"R" 1 "A" 53
"R" 1 "A" 54
"R" 1 "A" 55
"R" 1 "A" 56
"R" 1 "A" 57
"R" 1 "A" 58
"R" 1 "A" 59
"R" 1 "A" 60
"R" 1 "A" 61
"R" 1 "A" 62
"R" 1 "A" 63
"R" 1 "A" 64
"R" 1 "A" 65
"R" 1 "A" 66
"R" 1 "A" 67
"R" 1 "A" 68
"R" 1 "A" 69
"R" 1 "A" 70
"R" 1 "A" 71
"R" 1 "A" 72
"R" 1 "A" 73
"R" 1 "A" 74
"R" 1 "A" 75
"R" 1 "A" 76
"R" 1 "A" 77
"R" 1 "A" 78
"R" 1 "A" 79
"R" 1 "A" 80
"R" 1 "A" 81
"R" 1 "A" 82
"R" 1 "A" 83
"R" 1 "A" 84
"R" 1 "A" 85
"R" 1 "A" 86
"R" 1 "A" 87
"R" 1 "A" 88
"R" 1 "A" 89
"R" 1 "A" 90
"R" 1 "A" 91
"R" 1 "A" 92
"R" 1 "A" 93
"R" 1 "A" 94
"R" 1 "A" 95
"R" 1 "A" 96
"R" 1 "A" 97
"R" 1 "A" 98
"R" 1 "A" 99
"R" 1 "A" 100
"R" 1 "A" 101
"R" 1 "A" 102
"R" 1 "A" 103
"R" 1 "A" 104
"R" 1 "A" 105
"R" 1 "A" 106
"R" 1 "A" 107
"R" 1 "A" 108
"R" 1 "A" 109
"R" 1 "A" 110
"R" 1 "A" 111
"R" 1 "A" 112
"R" 1 "A" 113
"R" 1 "A" 114
"R" 1 "A" 115
"R" 1 "A" 116
"R" 1 "A" 117
"R" 1 "A" 118
"R" 1 "A" 119
"R" 1 "A" 120
"R" 1 "A" 121
"R" 1 "A" 122
"R" 1 "A" 123
"R" 1 "A" 124
"R" 1 "A" 125
"R" 1 "A" 126
"R" 1 "A" 127
"R" 1 "A" 128
"R" 1 "A" 129
"R" 1 "A" 130
"R" 1 "A" 131
"R" 1 "A" 132
"R" 1 "A" 133
"R" 1 "A" 134
"R" 1 "A" 135
"R" 1 "A" 136
"R" 1 "A" 137
"R" 1 "A" 138
"R" 1 "A" 139
"R" 1 "A" 140
"R" 1 "A" 141
"R" 1 "A" 142
"R" 1 "A" 143
"R" 1 "A" 144
"R" 1 "A" 145
"R" 1 "A" 146
"R" 1 "A" 147
"R" 1 "A" 148
"R" 1 "A" 149
"R" 1 "A" 150
"R" 1 "A" 151
"R" 1 "A" 152
"R" 1 "A" 153
"R" 1 "A" 154
"R" 1 "A" 155
"R" 1 "A" 156
"R" 1 "A" 157
"R" 1 "A" 158
"R" 1 "A" 159
"R" 1 "A" 160
"R" 1 "A" 161
"R" 1 "A" 162
"R" 1 "A" 163
"R" 1 "A" 164
"R" 1 "A" 165
"R" 1 "A" 166
"R" 1 "A" 167
"R" 1 "A" 168
"R" 1 "A" 169
"R" 1 "A" 170
"R" 1 "A" 171
"R" 1 "A" 172
"R" 1 "A" 173
"R" 1 "A" 174
"R" 1 "A" 175
"R" 1 "A" 176
"R" 1 "A" 177
"R" 1 "A" 178
"R" 1 "A" 179
"R" 1 "A" 180
"R" 1 "A" 181
"R" 1 "A" 182
"R" 1 "A" 183
"R" 1 "A" 184
"R" 1 "A" 185
"R" 1 "A" 186
"R" 1 "A" 187
"R" 1 "A" 188
"R" 1 "A" 189
"R" 1 "A" 190
"R" 1 "A" 191
"R" 1 "A" 192
"R" 1 "A" 193
"R" 1 "A" 194
"R" 1 "A" 195
"R" 1 "A" 196
!entry.GRA.unit.name single str
"min2.pdb"
!entry.GRA.unit.positions table dbl x dbl y dbl z
2.062000 16.176000 75.379000
2.065000 15.719000 74.400000
2.048000 17.559000 75.381000
2.042000 18.041000 74.419000
2.035000 18.274000 76.583000
2.040000 17.549000 77.784000
2.053000 16.137000 77.786000
2.063000 15.436000 76.564000
2.069000 14.036000 76.565000
2.078000 13.302000 75.374000
2.079000 13.774000 74.399000
2.081000 11.932000 75.369000
2.082000 11.462000 74.400000
2.073000 11.197000 76.564000
2.067000 11.912000 77.776000
2.066000 13.315000 77.775000
2.062000 14.024000 78.993000
2.057000 15.422000 78.989000
2.054000 16.116000 80.209000
2.043000 17.517000 80.213000
2.033000 18.230000 79.007000
2.017000 19.631000 79.018000
2.007000 20.356000 77.821000
2.019000 19.684000 76.588000
2.014000 20.458000 75.411000
2.023000 20.016000 74.426000
1.994000 21.848000 75.459000
1.991000 22.424000 74.536000
1.984000 22.500000 76.680000
1.975000 23.587000 76.714000
1.990000 21.758000 77.853000
1.983000 22.430000 79.074000
1.979000 23.517000 79.091000
1.993000 21.716000 80.258000
1.988000 22.401000 81.464000
1.984000 23.489000 81.472000
2.010000 20.316000 80.240000
2.023000 19.602000 81.442000
2.038000 18.209000 81.434000
2.049000 17.499000 82.642000
2.060000 16.105000 82.639000
2.061000 15.410000 81.422000
2.067000 14.011000 81.419000
2.066000 13.313000 80.201000
2.066000 11.911000 80.204000
2.064000 11.207000 78.986000
2.058000 9.804000 78.984000
2.056000 9.091000 77.776000
2.066000 9.794000 76.562000
2.069000 9.056000 75.370000
2.072000 9.516000 74.396000
2.058000 7.677000 75.375000
2.056000 7.196000 74.409000
2.042000 6.955000 76.569000
2.044000 7.685000 77.774000
2.032000 6.992000 79.000000
2.041000 7.711000 80.203000
2.055000 9.102000 80.202000
2.062000 9.817000 81.418000
2.068000 11.209000 81.413000
2.071000 11.913000 82.633000
2.072000 13.307000 82.633000
2.072000 14.009000 83.851000
2.067000 15.399000 83.852000
2.063000 16.101000 85.070000
2.052000 17.495000 85.071000
2.043000 18.197000 83.858000
2.026000 19.593000 83.860000
2.015000 20.296000 82.654000
1.996000 21.697000 82.665000
1.986000 22.388000 83.868000
1.977000 23.477000 83.863000
1.991000 21.689000 85.065000
1.973000 22.388000 86.274000
1.954000 23.472000 86.265000
2.013000 20.294000 85.071000
2.023000 19.590000 86.280000
2.043000 18.196000 86.282000
2.049000 17.502000 87.499000
2.061000 16.101000 87.498000
2.067000 15.400000 86.283000
2.072000 14.006000 86.286000
2.074000 13.301000 85.065000
2.074000 11.911000 85.068000
2.072000 11.209000 83.847000
2.066000 9.817000 83.848000
2.059000 9.111000 82.630000
2.044000 7.721000 82.635000
2.033000 7.013000 81.420000
2.010000 5.618000 81.431000
1.998000 4.907000 80.222000
2.012000 5.598000 79.005000
2.005000 4.872000 77.804000
2.023000 5.548000 76.573000
2.019000 4.775000 75.398000
2.032000 5.219000 74.410000
1.997000 3.387000 75.438000
1.989000 2.811000 74.521000
1.979000 2.730000 76.660000
1.962000 1.645000 76.690000
1.983000 3.472000 77.836000
1.964000 2.794000 79.050000
1.945000 1.709000 79.069000
1.971000 3.511000 80.242000
1.951000 2.819000 81.446000
1.928000 1.733000 81.449000
1.961000 3.526000 82.643000
1.934000 2.824000 83.849000
1.901000 1.742000 83.840000
1.994000 4.920000 82.639000
2.007000 5.626000 83.845000
2.034000 7.017000 83.846000
2.045000 7.722000 85.060000
2.061000 9.111000 85.062000
2.066000 9.813000 86.277000
2.072000 11.207000 86.280000
2.072000 11.907000 87.496000
2.072000 13.302000 87.497000
2.069000 14.006000 88.715000
2.063000 15.407000 88.715000
2.057000 16.118000 89.926000
2.044000 17.517000 89.924000
2.037000 18.208000 88.709000
2.016000 19.606000 88.701000
2.006000 20.298000 87.488000
1.980000 21.692000 87.477000
1.958000 22.394000 88.674000
1.933000 23.479000 88.668000
1.971000 21.714000 89.893000
1.953000 22.508000 91.090000
1.976000 21.843000 92.364000
2.007000 20.381000 92.315000
2.037000 19.672000 93.520000
2.057000 18.294000 93.533000
2.089000 17.837000 94.514000
2.054000 20.181000 94.473000
1.968000 22.628000 93.487000
1.946000 23.713000 93.402000
1.987000 22.232000 94.492000
1.927000 23.592000 91.041000
2.000000 20.323000 89.904000
2.014000 19.648000 91.127000
2.036000 18.239000 91.131000
2.051000 17.541000 92.352000
2.062000 16.137000 92.348000
2.074000 15.413000 93.545000
2.078000 14.031000 93.543000
2.074000 13.301000 92.352000
2.094000 13.571000 94.518000
2.085000 15.880000 94.515000
2.062000 15.418000 91.142000
2.068000 14.011000 91.138000
2.070000 13.303000 89.927000
2.070000 11.902000 89.927000
2.069000 11.198000 88.712000
2.063000 9.801000 88.708000
2.059000 9.103000 87.494000
2.043000 7.710000 87.488000
2.033000 7.012000 86.272000
2.002000 5.621000 86.265000
1.986000 4.919000 85.057000
1.945000 3.525000 85.052000
1.912000 2.824000 86.250000
1.867000 1.739000 86.243000
1.934000 3.516000 87.459000
1.908000 2.813000 88.660000
1.860000 1.725000 88.646000
1.981000 4.911000 87.473000
2.001000 5.599000 88.689000
2.031000 6.997000 88.695000
2.043000 7.686000 89.914000
2.058000 9.088000 89.919000
2.065000 9.783000 91.135000
2.070000 11.189000 91.135000
2.076000 11.900000 92.352000
2.088000 11.160000 93.539000
2.110000 11.625000 94.517000
2.084000 9.790000 93.539000
2.100000 9.314000 94.509000
2.069000 9.063000 92.342000
2.057000 7.655000 92.339000
2.037000 6.963000 91.122000
2.010000 5.558000 91.111000
1.986000 4.880000 89.888000
1.942000 3.489000 89.871000
1.927000 2.690000 91.070000
1.886000 1.610000 91.021000
1.971000 3.357000 92.351000
1.968000 2.570000 93.465000
1.998000 2.965000 94.475000
1.933000 1.484000 93.385000
2.007000 4.815000 92.301000
2.041000 5.524000 93.505000
2.055000 5.015000 94.458000
2.065000 6.906000 93.520000
2.099000 7.358000 94.503000
!entry.GRA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
0 0 0 0 0 0
!entry.GRA.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
"GRA" 1 197 1 "?" 0
!entry.GRA.unit.residuesPdbSequenceNumber array int
0
!entry.GRA.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.GRA.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0
0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
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?
?
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Received on Thu Feb 26 2015 - 23:00:02 PST
