From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Jun 09 2016 - 09:36:37 CDT
It would help if you were more specific, i.e., what steps you took and what files were generated and then loaded. My guess is that you are using an older version of VMD that had trouble with long atom types, which CGENFF uses. Try downloading the latest VMD and trying again. If that doesn’t work, posting the exact steps will help someone attempt to reproduce it.
Best,
JC
> On Jun 7, 2016, at 9:34 PM, Benjamin Hill <ben.luc.chem_at_gmail.com> wrote:
>
> Hello,
> I am using the ParamChem website to generate CGENFF parameters for a NTP molecule. In the example here, I am just trying to work with ATP. The ParamChem website gave me a toppar (topology + parameter) file to work with. When I analyze the file, indeed, the charge is -4.000. However, when I try to 'compile' (... add water, ions, etc...) using VMD, it should give a charge of something very near 0.000 (--- Due to the addition of ions, in order to neutralize the system).
> However it is not -- it is saying the charge of this one molecule system (with water and ions) is 0.1400. I cannot figure out what is going on. Please help? FYI: When I work with other molecules (not obtained from CGENFF all is ok.... problem only exists here.
>
> Below are:
> 1) the PDB coordinates
> 2) the Toppar file
>
> ### PDB FILE ####
>
> HETATM 1 P1 ATX 1 57.176 -8.670 57.837 0.00 0.00 P
> HETATM 2 P2 ATX 1 59.625 -7.965 58.722 0.00 0.00 P
> HETATM 3 P3 ATX 1 61.020 -8.164 56.488 0.00 0.00 P
> HETATM 4 C1 ATX 1 53.344 -9.060 65.812 0.00 0.00 C
> HETATM 5 N1 ATX 1 54.373 -8.726 66.614 0.00 0.00 N
> HETATM 6 O1 ATX 1 56.108 -8.970 58.878 0.00 0.00 O
> HETATM 7 C2 ATX 1 54.502 -9.161 63.977 0.00 0.00 C
> HETATM 8 N2 ATX 1 53.278 -9.273 64.503 0.00 0.00 N
> HETATM 9 O2 ATX 1 54.542 -10.548 60.678 0.00 0.00 O
> HETATM 10 C3 ATX 1 55.678 -8.918 64.569 0.00 0.00 C
> HETATM 11 N3 ATX 1 56.655 -8.847 63.593 0.00 0.00 N
> HETATM 12 O3 ATX 1 51.872 -9.168 59.347 0.00 0.00 O
> HETATM 13 C4 ATX 1 55.590 -8.667 65.971 0.00 0.00 C
> HETATM 14 N4 ATX 1 54.709 -9.163 62.626 0.00 0.00 N
> HETATM 15 O4 ATX 1 53.075 -7.181 61.227 0.00 0.00 O
> HETATM 16 C5 ATX 1 56.081 -8.994 62.432 0.00 0.00 C
> HETATM 17 N5 ATX 1 56.628 -8.165 66.780 0.00 0.00 N
> HETATM 18 O5 ATX 1 57.920 -9.932 57.357 0.00 0.00 O1-
> HETATM 19 C6 ATX 1 55.471 -10.289 58.830 0.00 0.00 C
> HETATM 20 O6 ATX 1 60.179 -7.008 59.750 0.00 0.00 O1-
> HETATM 21 C7 ATX 1 54.047 -10.208 59.305 0.00 0.00 C
> HETATM 22 O7 ATX 1 62.302 -8.002 57.220 0.00 0.00 O
> HETATM 23 C8 ATX 1 53.267 -8.880 59.288 0.00 0.00 C
> HETATM 24 O8 ATX 1 56.599 -7.713 56.844 0.00 0.00 O
> HETATM 25 C9 ATX 1 53.855 -8.283 60.599 0.00 0.00 C
> HETATM 26 O9 ATX 1 59.879 -9.440 58.922 0.00 0.00 O
> HETATM 27 C10 ATX 1 53.897 -9.540 61.517 0.00 0.00 C
> HETATM 28 O10 ATX 1 60.495 -9.554 56.344 0.00 0.00 O1-
> HETATM 29 O11 ATX 1 58.059 -7.809 58.826 0.00 0.00 O
> HETATM 30 O12 ATX 1 59.896 -7.429 57.224 0.00 0.00 O
> HETATM 31 O13 ATX 1 60.966 -7.475 55.164 0.00 0.00 O
> HETATM 32 H1 ATX 1 57.063 -9.096 61.249 0.00 0.00 H
> HETATM 33 H2 ATX 1 52.456 -8.989 66.440 0.00 0.00 H
> HETATM 34 H3 ATX 1 55.437 -10.551 57.773 0.00 0.00 H
> HETATM 35 H4 ATX 1 56.038 -10.905 59.526 0.00 0.00 H
> HETATM 36 H5 ATX 1 53.352 -10.988 58.995 0.00 0.00 H
> HETATM 37 H6 ATX 1 53.283 -8.236 58.409 0.00 0.00 H
> HETATM 38 H7 ATX 1 51.742 -10.061 59.671 0.00 0.00 H
> HETATM 39 H8 ATX 1 54.903 -7.483 60.493 0.00 0.00 H
> HETATM 40 H9 ATX 1 52.451 -7.549 61.855 0.00 0.00 H
> HETATM 41 H10 ATX 1 52.975 -9.948 61.929 0.00 0.00 H
> HETATM 42 H11 ATX 1 57.360 -7.603 66.372 0.00 0.00 H
> HETATM 43 H12 ATX 1 56.638 -8.367 67.771 0.00 0.00 H
>
>
>
> #### Toppar file: ########
>
> * Toppar stream file generated by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> * For use with CGenFF version 3.0.1
> *
>
> read rtf card append
> * Topologies generated by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> *
> 36 1
>
> ! "penalty" is the highest penalty score of the associated parameters.
> ! Penalties lower than 10 indicate the analogy is fair; penalties between 10
> ! and 50 mean some basic validation is recommended; penalties higher than
> ! 50 indicate poor analogy and mandate extensive validation/optimization.
>
> RESI ATX -4.000 ! param penalty= 0.000 ; charge penalty= 0.000
> GROUP ! CHARGE CH_PENALTY
> ATOM N1 NG2R62 -0.742 ! 0.000
> ATOM C1 CG2R64 0.500 ! 0.000
> ATOM N2 NG2R62 -0.753 ! 0.000
> ATOM C2 CG2RC0 0.429 ! 0.000
> ATOM C3 CG2RC0 0.286 ! 0.000
> ATOM C4 CG2R64 0.456 ! 0.000
> ATOM N3 NG2R50 -0.712 ! 0.000
> ATOM C5 CG2R53 0.340 ! 0.000
> ATOM N4 NG2R51 -0.052 ! 0.000
> ATOM P1 PG1 1.504 ! 0.000
> ATOM P2 PG1 1.505 ! 0.000
> ATOM P3 PG2 1.107 ! 0.000
> ATOM C6 CG321 -0.081 ! 0.000
> ATOM O1 OG303 -0.617 ! 0.000
> ATOM C7 CG3C51 0.113 ! 0.000
> ATOM O2 OG3C51 -0.416 ! 0.000
> ATOM C8 CG3C51 0.142 ! 0.000
> ATOM O3 OG311 -0.648 ! 0.000
> ATOM C9 CG3C51 0.139 ! 0.000
> ATOM O4 OG311 -0.648 ! 0.000
> ATOM C10 CG3C51 0.114 ! 0.000
> ATOM O5 OG2P1 -0.817 ! 0.000
> ATOM O6 OG2P1 -0.837 ! 0.000
> ATOM O7 OG2P1 -0.900 ! 0.000
> ATOM O8 OG2P1 -0.817 ! 0.000
> ATOM O9 OG2P1 -0.837 ! 0.000
> ATOM O10 OG2P1 -0.900 ! 0.000
> ATOM O11 OG304 -0.733 ! 0.000
> ATOM O12 OG304 -0.852 ! 0.000
> ATOM O13 OG2P1 -0.900 ! 0.000
> ATOM N5 NG2S3 -0.772 ! 0.000
> ATOM H1 HGR52 0.130 ! 0.000
> ATOM H2 HGR62 0.129 ! 0.000
> ATOM H3 HGA2 0.090 ! 0.000
> ATOM H4 HGA2 0.090 ! 0.000
> ATOM H5 HGA1 0.090 ! 0.000
> ATOM H6 HGA1 0.090 ! 0.000
> ATOM H7 HGP1 0.420 ! 0.000
> ATOM H8 HGA1 0.090 ! 0.000
> ATOM H9 HGP1 0.420 ! 0.000
> ATOM H10 HGA1 0.090 ! 0.000
> ATOM H11 HGP4 0.380 ! 0.000
> ATOM H12 HGP4 0.380 ! 0.000
>
> BOND N1 C1
> BOND N1 C4
> BOND C1 H2
> BOND N2 C2
> BOND C2 N4
> BOND C3 C4
> BOND C3 N3
> BOND C5 N4
> BOND C5 H1
> BOND N4 C10
> BOND P1 O1
> BOND P1 O8
> BOND P1 O11
> BOND P2 O9
> BOND P2 O11
> BOND P2 O12
> BOND P3 O7
> BOND P3 O12
> BOND C6 O1
> BOND C6 C7
> BOND C6 H3
> BOND C6 H4
> BOND C7 O2
> BOND C7 C8
> BOND C7 H5
> BOND O2 C10
> BOND C8 O3
> BOND C8 C9
> BOND C8 H6
> BOND O3 H7
> BOND C9 O4
> BOND C9 C10
> BOND C9 H8
> BOND O4 H9
> BOND C10 H10
> BOND P3 O13
> BOND P3 O10
> BOND P2 O6
> BOND P1 O5
> BOND N3 C5
> BOND C4 N5
> BOND C2 C3
> BOND C1 N2
> BOND N5 H11
> BOND N5 H12
> IMPR C4 C3 N1 N5
> IMPR N5 H12 H11 C4
>
> END
>
> read param card flex append
> * Parameters generated by analogy by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> *
>
> ! Penalties lower than 10 indicate the analogy is fair; penalties between 10
> ! and 50 mean some basic validation is recommended; penalties higher than
> ! 50 indicate poor analogy and mandate extensive validation/optimization.
>
> BONDS
> CG2R53 NG2R50 400.00 1.3200 ! PROT his, ADM JR., 7/20/89
> CG2R53 NG2R51 320.00 1.3740 ! NA A, adm jr. 11/97
> CG2R53 HGR52 340.00 1.0900 ! PROT his, adm jr., 6/28/29
> CG2R64 CG2RC0 360.00 1.3580 ! NA A, adm jr. 11/97
> CG2R64 NG2R62 400.00 1.3420 ! NA A, adm jr. 11/97
> CG2R64 NG2S3 360.00 1.3660 ! NA C,A,G JWK, adm jr. 10/2/91
> CG2R64 HGR62 380.00 1.0900 ! NA G,A, JWK par_a7 9/30/91
> CG2RC0 CG2RC0 360.00 1.3850 ! INDO/TRP
> CG2RC0 NG2R50 310.00 1.3650 ! NA G, adm jr. 11/97
> CG2RC0 NG2R51 300.00 1.3750 ! NA A, adm jr. 11/97
> CG2RC0 NG2R62 350.00 1.3150 ! NA G, adm jr. 11/97
> CG321 CG3C51 222.50 1.5280 ! TF2M, viv
> CG321 OG303 320.00 1.4400 ! PROTNA serine/threonine phosphate
> CG321 HGA2 309.00 1.1110 ! PROT alkane update, adm jr., 3/2/92
> CG3C51 CG3C51 195.00 1.5180 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv
> CG3C51 NG2R51 220.00 1.4580 ! NA G/T/U
> CG3C51 OG311 428.00 1.4200 ! PROT methanol vib fit EMB 11/21/89
> CG3C51 OG3C51 350.00 1.4250 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv
> CG3C51 HGA1 307.00 1.1000 ! THF, THF neutron diffr., 5/30/06, viv
> NG2S3 HGP4 488.00 1.0000 ! NA A,C,G, JWK, adm jr. 7/24/91
> OG2P1 PG1 500.00 1.5100 ! MP_1 reorganization, kevo
> OG2P1 PG2 400.00 1.5200 ! MP_2 reorganization, kevo
> OG303 PG1 190.00 1.6500 ! MP_1 reorganization, kevo
> OG304 PG1 330.00 1.6750 ! PPI1, PPI2, METP reorganization, kevo ! pulls against attraction
> OG304 PG2 300.00 1.7150 ! PPI1, METP reorganization, kevo ! pulls against very strong attraction
> OG311 HGP1 545.00 0.9600 ! PROT EMB 11/21/89 methanol vib fit; og tested on MeOH EtOH,...
>
> ANGLES
> NG2R50 CG2R53 NG2R51 100.00 113.00 ! NA Gua 5R)
> NG2R50 CG2R53 HGR52 39.00 124.80 ! NA Ade h8, G,A
> NG2R51 CG2R53 HGR52 40.00 122.20 ! NA Gua h8 (NN4 CG2R53HN3 124.8)
> CG2RC0 CG2R64 NG2R62 60.00 110.70 ! NA Ade 6R)
> CG2RC0 CG2R64 NG2S3 50.00 118.60 ! NA Ade
> NG2R62 CG2R64 NG2R62 60.00 128.00 ! NA Ade 6R) %%% TEST 133.0 -> 122.2 %%%
> NG2R62 CG2R64 NG2S3 95.00 122.40 ! NA Gua
> NG2R62 CG2R64 HGR62 38.00 116.00 ! NA Ade h2 %%% TEST 113.5 -> 118.9 %%%
> CG2R64 CG2RC0 CG2RC0 60.00 121.00 ! NA Ade 6R) bridgeC5
> CG2R64 CG2RC0 NG2R50 100.00 129.00 ! NA Ade bridgeC5
> CG2RC0 CG2RC0 NG2R50 100.00 110.00 ! NA Ade 5R) bridgeC5
> CG2RC0 CG2RC0 NG2R51 100.00 105.70 ! NA Ade 5R) bridgeC4
> CG2RC0 CG2RC0 NG2R62 60.00 127.40 ! NA Ade 6R) bridgeC4
> NG2R51 CG2RC0 NG2R62 100.00 126.90 ! NA Ade bridgeC4
> CG3C51 CG321 OG303 75.70 110.10 ! LIPID acetic acid
> CG3C51 CG321 HGA2 34.60 110.10 22.53 2.17900 ! TF2M viv
> OG303 CG321 HGA2 60.00 109.50 ! PROTNA Thr-Phos
> HGA2 CG321 HGA2 35.50 109.00 5.40 1.80200 ! PROT alkane update, adm jr., 3/2/92
> CG321 CG3C51 CG3C51 58.00 115.00 8.00 2.56100 ! TF2M viv
> CG321 CG3C51 OG3C51 45.00 111.50 ! TF2M, viv
> CG321 CG3C51 HGA1 34.60 110.10 22.53 2.17900 ! TF2M viv
> CG3C51 CG3C51 CG3C51 58.00 109.50 11.16 2.56100 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv
> CG3C51 CG3C51 NG2R51 110.00 111.00 ! NA T/U/G, Arabinose (NF)
> CG3C51 CG3C51 OG311 75.70 110.10 ! PROT MeOH, EMB, 10/10/89
> CG3C51 CG3C51 OG3C51 45.00 111.10 ! THF 10/21/05, viv
> CG3C51 CG3C51 HGA1 35.00 111.40 22.53 2.17900 ! TF2M, viv
> NG2R51 CG3C51 OG3C51 140.00 108.00 ! NA
> NG2R51 CG3C51 HGA1 43.00 111.00 ! NA From HGA1 CG3C51 NN2
> OG311 CG3C51 HGA1 45.90 108.89 ! PROT MeOH, EMB, 10/10/89
> OG3C51 CG3C51 HGA1 70.00 107.30 ! THF 10/21/05, viv
> CG2R53 NG2R50 CG2RC0 120.00 103.80 ! NA Gua 5R)
> CG2R53 NG2R51 CG2RC0 100.00 107.20 ! NA Gua 5R)
> CG2R53 NG2R51 CG3C51 45.00 126.30 ! NA G
> CG2RC0 NG2R51 CG3C51 45.00 126.50 ! NA G
> CG2R64 NG2R62 CG2R64 90.00 117.80 ! NA Ade 6R) adm jr. 11/97
> CG2R64 NG2R62 CG2RC0 90.00 115.10 ! NA Ade 6R) %%% TEST 110.1 -> 120.9 %%%
> CG2R64 NG2S3 HGP4 40.00 121.50 ! NA Ade h61,h62, C,A,G
> HGP4 NG2S3 HGP4 31.00 117.00 ! NA Ade C,A,G
> CG321 OG303 PG1 20.00 120.00 35.00 2.33000 ! NA !Reorganization: PC and others
> PG1 OG304 PG1 45.00 143.00 40.00 3.25000 ! PPI2, METP reorganization, kevo
> PG1 OG304 PG2 45.00 139.50 40.00 3.05000 ! PPI1, METP reorganization, kevo
> CG3C51 OG311 HGP1 50.00 109.00 ! par_Sugars, CC315x OC311 HCP1; was 57.5 106
> CG3C51 OG3C51 CG3C51 95.00 111.00 ! THF 10/21/05, viv
> OG2P1 PG1 OG2P1 104.00 120.00 ! MP_1 reorganization, kevo
> OG2P1 PG1 OG303 98.90 107.50 ! MP_1 reorganization, kevo
> OG2P1 PG1 OG304 88.90 111.60 ! NA nad/ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1, PPI2
> OG303 PG1 OG304 48.10 105.00 ! PPI1, PPI2, METP reorganization, kevo
> OG304 PG1 OG304 48.10 107.50 ! METP reorganization, kevo
> OG2P1 PG2 OG2P1 104.00 121.00 ! MP_2 reorganization, kevo
> OG2P1 PG2 OG304 88.90 111.60 ! NA nad/ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1, PPI2
>
> DIHEDRALS
> NG2R51 CG2R53 NG2R50 CG2RC0 14.0000 2 180.00 ! NA A
> HGR52 CG2R53 NG2R50 CG2RC0 5.2000 2 180.00 ! NA A
> NG2R50 CG2R53 NG2R51 CG2RC0 6.0000 2 180.00 ! NA A
> NG2R50 CG2R53 NG2R51 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage
> HGR52 CG2R53 NG2R51 CG2RC0 5.6000 2 180.00 ! NA G
> HGR52 CG2R53 NG2R51 CG3C51 0.0000 2 180.00 ! NA, glycosyl linkage
> NG2R62 CG2R64 CG2RC0 CG2RC0 1.8000 2 180.00 ! NA A
> NG2R62 CG2R64 CG2RC0 NG2R50 2.0000 2 180.00 ! NA A
> NG2S3 CG2R64 CG2RC0 CG2RC0 4.0000 2 180.00 ! NA A
> NG2S3 CG2R64 CG2RC0 NG2R50 0.0000 2 180.00 ! NA A
> CG2RC0 CG2R64 NG2R62 CG2R64 1.8000 2 180.00 ! NA A
> NG2R62 CG2R64 NG2R62 CG2R64 1.8000 2 180.00 ! NA A
> NG2R62 CG2R64 NG2R62 CG2RC0 2.0000 2 180.00 ! NAMODEL guanine tautomer
> NG2S3 CG2R64 NG2R62 CG2R64 1.8000 2 180.00 ! NA A
> HGR62 CG2R64 NG2R62 CG2R64 8.5000 2 180.00 ! NA A
> HGR62 CG2R64 NG2R62 CG2RC0 8.5000 2 180.00 ! NA A
> CG2RC0 CG2R64 NG2S3 HGP4 0.5000 2 180.00 ! NA A
> NG2R62 CG2R64 NG2S3 HGP4 1.0000 2 180.00 ! NA C
> CG2R64 CG2RC0 CG2RC0 NG2R51 7.0000 2 180.00 ! NA A
> CG2R64 CG2RC0 CG2RC0 NG2R62 2.0000 2 180.00 ! NA A
> NG2R50 CG2RC0 CG2RC0 NG2R51 10.0000 2 180.00 ! NA G
> NG2R50 CG2RC0 CG2RC0 NG2R62 7.0000 2 180.00 ! NA A
> CG2R64 CG2RC0 NG2R50 CG2R53 2.0000 2 180.00 ! NA A
> CG2RC0 CG2RC0 NG2R50 CG2R53 6.0000 2 180.00 ! NA G
> CG2RC0 CG2RC0 NG2R51 CG2R53 6.0000 2 180.00 ! NA G
> CG2RC0 CG2RC0 NG2R51 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage
> NG2R62 CG2RC0 NG2R51 CG2R53 2.0000 2 180.00 ! NA G
> NG2R62 CG2RC0 NG2R51 CG3C51 11.0000 2 180.00 ! NA, glycosyl linkage
> CG2RC0 CG2RC0 NG2R62 CG2R64 0.2000 2 180.00 ! NA G
> NG2R51 CG2RC0 NG2R62 CG2R64 2.0000 2 180.00 ! NA G
> OG303 CG321 CG3C51 CG3C51 2.5000 1 180.00 ! NA, sugar
> OG303 CG321 CG3C51 CG3C51 0.4000 2 0.00 ! NA, sugar
> OG303 CG321 CG3C51 CG3C51 0.8000 3 180.00 ! NA, sugar
> OG303 CG321 CG3C51 CG3C51 0.2000 4 180.00 ! NA, sugar
> OG303 CG321 CG3C51 OG3C51 3.4000 1 180.00 ! NA, sugar
> OG303 CG321 CG3C51 HGA1 0.1950 3 0.00 ! NA, sugar
> HGA2 CG321 CG3C51 CG3C51 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv
> HGA2 CG321 CG3C51 OG3C51 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv
> HGA2 CG321 CG3C51 HGA1 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell, tf2m viv
> CG3C51 CG321 OG303 PG1 0.6000 1 180.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr
> CG3C51 CG321 OG303 PG1 0.6500 2 0.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr
> CG3C51 CG321 OG303 PG1 0.0500 3 0.00 ! B5SP carbocyclic sugars reset to EP_2 phospho-ser/thr
> HGA2 CG321 OG303 PG1 0.0000 3 0.00 ! NA dmp !Reorganization: PC and others
> CG321 CG3C51 CG3C51 CG3C51 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv
> CG321 CG3C51 CG3C51 OG311 0.1400 3 0.00 ! PROT, hydroxyl wild card
> CG321 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv
> CG3C51 CG3C51 CG3C51 CG3C51 0.4100 3 180.00 ! cpen, cyclopentane, viv 10/4/05
> CG3C51 CG3C51 CG3C51 NG2R51 0.0000 3 0.00 ! NA, glycosyl linkage
> CG3C51 CG3C51 CG3C51 OG311 0.2000 3 0.00 ! par22, X CT1 CT2 X; erh 3/08
> CG3C51 CG3C51 CG3C51 OG3C51 0.0000 3 0.00 ! THF, 05/30/06, viv
> CG3C51 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv
> NG2R51 CG3C51 CG3C51 OG311 0.0000 3 0.00 ! NA Guanine and uracil
> NG2R51 CG3C51 CG3C51 HGA1 0.0000 3 0.00 ! NA, glycosyl linkage
> OG311 CG3C51 CG3C51 OG311 0.0000 3 0.00 ! NA bkb
> OG311 CG3C51 CG3C51 OG3C51 0.2000 3 0.00 ! NA, sugar
> OG311 CG3C51 CG3C51 OG3C51 0.6000 4 180.00 ! NA, sugar
> OG311 CG3C51 CG3C51 OG3C51 0.3000 5 0.00 ! NA, sugar
> OG311 CG3C51 CG3C51 OG3C51 0.5000 6 0.00 ! NA, sugar
> OG311 CG3C51 CG3C51 HGA1 0.1950 3 0.00 ! NA, sugar
> OG3C51 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf viv
> HGA1 CG3C51 CG3C51 HGA1 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell, thf, viv
> CG3C51 CG3C51 NG2R51 CG2R53 0.0000 3 180.00 ! NA, glycosyl linkage
> CG3C51 CG3C51 NG2R51 CG2RC0 0.0000 3 0.00 ! NA, glycosyl linkage
> OG3C51 CG3C51 NG2R51 CG2R53 1.1000 1 0.00 ! NA, glycosyl linkage
> OG3C51 CG3C51 NG2R51 CG2RC0 1.1000 1 180.00 ! NA, glycosyl linkage
> OG3C51 CG3C51 NG2R51 CG2RC0 0.2000 3 0.00 ! NA, glycosyl linkage
> HGA1 CG3C51 NG2R51 CG2R53 0.2500 2 180.00 ! NA, glycosyl linkage 0.25 2 180 to compensate for removal of OG3C51 CG3C51 NG2R51 CG2R51 0.5 2 -70
> HGA1 CG3C51 NG2R51 CG2R53 0.1950 3 0.00 ! NA, glycosyl linkage
> HGA1 CG3C51 NG2R51 CG2RC0 0.2500 2 180.00 ! NA, glycosyl linkage 0.25 2 180 to compensate for removal of OG3C51 CG3C51 NG2R51 CG2R51 0.5 2 -70
> CG3C51 CG3C51 OG311 HGP1 0.2900 1 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1
> CG3C51 CG3C51 OG311 HGP1 0.6200 2 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1
> CG3C51 CG3C51 OG311 HGP1 0.0500 3 0.00 ! Team sugar, CC3151 CC3152 OC311 HCP1
> HGA1 CG3C51 OG311 HGP1 0.1800 3 0.00 ! Team sugar, HCP1 OC311 CC3151 HCA1
> CG321 CG3C51 OG3C51 CG3C51 0.3000 3 0.00 ! THF, 05/30/06, viv
> CG3C51 CG3C51 OG3C51 CG3C51 0.5000 3 0.00 ! THF, 05/30/06, viv
> NG2R51 CG3C51 OG3C51 CG3C51 0.0000 3 0.00 ! NA, sugar
> HGA1 CG3C51 OG3C51 CG3C51 0.3000 3 0.00 ! THF, 05/30/06, viv
> CG321 OG303 PG1 OG2P1 0.1000 3 0.00 ! NA dmp !Reorganization: PC and others
> CG321 OG303 PG1 OG304 1.2000 1 180.00 ! NA dmp !Reorganization:ADP
> CG321 OG303 PG1 OG304 0.1000 2 180.00 ! NA dmp !Reorganization:ADP
> CG321 OG303 PG1 OG304 0.1000 3 180.00 ! NA dmp !Reorganization:ADP
> PG1 OG304 PG1 OG2P1 0.1000 2 0.00 ! NA ppi2 !Reorganization:PPI2
> PG1 OG304 PG1 OG2P1 0.0300 3 0.00 ! NA ppi2 !Reorganization:PPI2
> PG1 OG304 PG1 OG303 0.0300 2 0.00 ! NA ppi2 !Reorganization:PPI2
> PG1 OG304 PG1 OG303 0.0300 3 0.00 ! NA ppi2 !Reorganization:PPI2
> PG1 OG304 PG1 OG304 0.0300 2 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize?
> PG1 OG304 PG1 OG304 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize?
> PG2 OG304 PG1 OG2P1 0.1000 2 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1
> PG2 OG304 PG1 OG2P1 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1
> PG2 OG304 PG1 OG304 0.0300 2 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize?
> PG2 OG304 PG1 OG304 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:METP re-optimize?
> PG1 OG304 PG2 OG2P1 0.0300 3 0.00 ! NA ppi, jjp1/adm jr. 7/95 !Reorganization:PPI1
>
> IMPROPERS
> CG2R64 CG2RC0 NG2R62 NG2S3 40.0000 0 0.00 ! NA A
> NG2S3 HGP4 HGP4 CG2R64 9.0000 0 0.00 ! NA GUA ADE CYT; from artificially planar 2APY, 2-aminopyridine parameter set (12/2010); xxwy & kevo
>
> END
> RETURN
>
>
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