[gmx-users] Error: number of atoms do not match
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 10 20:27:13 CEST 2008
h a wrote:
> *****************
>
> Now I'm actually studying protein polymer_surface interactions, using
> g43a1 forcefield . Can anybody explain whether should I use polymer
> model with only polar hydrogens or polymer model with all hydrogens ?
> What is the significance of these hydrogens.
I would suggest reading the papers that correspond to the Gromos96 force fields,
and united-atom force fields in general.
In addition to the original papers, see here (some references are included):
http://wiki.gromacs.org/index.php/GROMOS
-Justin
> In the .itp file(shown below) there are 130 atoms but total number of
> atoms in only polar hydrogens model is 80 same with no hydrogens model.
> Including all hydrogens I have 162 atoms. So what does this 130
> correspond to ?? ( actually I'm facing fatal error because of this
> consistency in number of atoms while doing EM )
> *******
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 CR1 1 STY CAB 1 -0.006 12.0110
> 2 HC 1 STY HAB 1 0.006 1.0080
> 3 CR1 1 STY CAC 2 -0.016 12.0110
> 4 HC 1 STY HAC 2 0.002 1.0080
> 5 CR1 1 STY CAD 2 -0.017 12.0110
> 6 HC 1 STY HAD 2 0.002 1.0080
> 7 CR1 1 STY CAE 2 -0.017 12.0110
> 8 HC 1 STY HAE 2 0.002 1.0080
> 9 CR1 1 STY CAF 2 -0.017 12.0110
> 10 HC 1 STY HAF 2 0.002 1.0080
> 11 C 1 STY CAA 2 -0.025 12.0110
> 12 CH1 1 STY CAG 2 0.067 13.0190
> 13 CH3 1 STY CAH 2 0.017 15.0350
> 14 CH2 1 STY CAP 3 0.000 14.0270
> 15 CH1 1 STY CAO 4 0.060 13.0190
> 16 C 1 STY CAI 4 -0.027 12.0110
> 17 CR1 1 STY CAJ 4 -0.018 12.0110
> 18 HC 1 STY HAK 4 0.001 1.0080
> 19 CR1 1 STY CAK 4 -0.018 12.0110
> 20 HC 1 STY HAL 4 0.002 1.0080
> 21 CR1 1 STY CAL 5 -0.016 12.0110
> 22 HC 1 STY HAM 5 0.003 1.0080
> 23 CR1 1 STY CAM 5 -0.016 12.0110
> 24 HC 1 STY HAN 5 0.003 1.0080
> 25 CR1 1 STY CAN 5 -0.016 12.0110
> 26 HC 1 STY HAO 5 0.003 1.0080
> 27 CH2 1 STY CAX 5 0.039 14.0270
> 28 CH1 1 STY CAW 6 0.060 13.0190
> 29 C 1 STY CAQ 6 -0.027 12.0110
> 30 CR1 1 STY CAR 6 -0.018 12.0110
> 31 HC 1 STY HAS 6 0.001 1.0080
> 32 CR1 1 STY CAS 6 -0.018 12.0110
> 33 HC 1 STY HAT 6 0.002 1.0080
> 34 CR1 1 STY CAT 7 -0.016 12.0110
> 35 HC 1 STY HAU 7 0.003 1.0080
> 36 CR1 1 STY CAU 7 -0.016 12.0110
> 37 HC 1 STY HAV 7 0.003 1.0080
> 38 CR1 1 STY CAV 7 -0.016 12.0110
> 39 HC 1 STY HAW 7 0.003 1.0080
> 40 CH2 1 STY CBF 7 0.039 14.0270
> 41 CH1 1 STY CBE 8 0.060 13.0190
> 42 C 1 STY CAY 8 -0.027 12.0110
> 43 CR1 1 STY CAZ 8 -0.018 12.0110
> 44 HC 1 STY HA0 8 0.001 1.0080
> 45 CR1 1 STY CBA 8 -0.018 12.0110
> 46 HC 1 STY HBA 8 0.002 1.0080
> 47 CR1 1 STY CBB 9 -0.016 12.0110
> 48 HC 1 STY HBB 9 0.003 1.0080
> 49 CR1 1 STY CBC 9 -0.016 12.0110
> 50 HC 1 STY HBC 9 0.003 1.0080
> 51 CR1 1 STY CBD 9 -0.016 12.0110
> 52 HC 1 STY HBD 9 0.003 1.0080
> 53 CH2 1 STY CBN 9 0.039 14.0270
> 54 CH1 1 STY CBM 10 0.060 13.0190
> 55 C 1 STY CBG 10 -0.027 12.0110
> 56 CR1 1 STY CBH 10 -0.018 12.0110
> 57 HC 1 STY HBH 10 0.001 1.0080
> 58 CR1 1 STY CBI 10 -0.018 12.0110
> 59 HC 1 STY HBI 10 0.002 1.0080
> 60 CR1 1 STY CBJ 11 -0.016 12.0110
> 61 HC 1 STY HBJ 11 0.003 1.0080
> 62 CR1 1 STY CBK 11 -0.016 12.0110
> 63 HC 1 STY HBK 11 0.003 1.0080
> 64 CR1 1 STY CBL 11 -0.016 12.0110
> 65 HC 1 STY HBL 11 0.003 1.0080
> 66 CH2 1 STY CBV 11 0.039 14.0270
> 67 CH1 1 STY CBU 12 0.060 13.0190
> 68 C 1 STY CBO 12 -0.027 12.0110
> 69 CR1 1 STY CBP 12 -0.018 12.0110
> 70 HC 1 STY HBP 12 0.001 1.0080
> 71 CR1 1 STY CBQ 12 -0.018 12.0110
> 72 HC 1 STY HBQ 12 0.002 1.0080
> 73 CR1 1 STY CBR 13 -0.016 12.0110
> 74 HC 1 STY HBR 13 0.003 1.0080
> 75 CR1 1 STY CBS 13 -0.016 12.0110
> 76 HC 1 STY HBS 13 0.003 1.0080
> 77 CR1 1 STY CBT 13 -0.016 12.0110
> 78 HC 1 STY HBT 13 0.003 1.0080
> 79 CH2 1 STY CCD 13 0.039 14.0270
> 80 CH1 1 STY CCC 14 0.060 13.0190
> 81 C 1 STY CBW 14 -0.027 12.0110
> 82 CR1 1 STY CBX 14 -0.018 12.0110
> 83 HC 1 STY HBX 14 0.001 1.0080
> 84 CR1 1 STY CBY 14 -0.018 12.0110
> 85 HC 1 STY HBY 14 0.002 1.0080
> 86 CR1 1 STY CBZ 15 -0.016 12.0110
> 87 HC 1 STY HBZ 15 0.003 1.0080
> 88 CR1 1 STY CCA 15 -0.016 12.0110
> 89 HC 1 STY HCA 15 0.003 1.0080
> 90 CR1 1 STY CCB 15 -0.016 12.0110
> 91 HC 1 STY HCB 15 0.003 1.0080
> 92 CH2 1 STY CCL 15 0.039 14.0270
> 93 CH1 1 STY CCK 16 0.060 13.0190
> 94 C 1 STY CCE 16 -0.027 12.0110
> 95 CR1 1 STY CCF 16 -0.018 12.0110
> 96 HC 1 STY HCF 16 0.001 1.0080
> 97 CR1 1 STY CCG 16 -0.018 12.0110
> 98 HC 1 STY HCG 16 0.002 1.0080
> 99 CR1 1 STY CCH 17 -0.016 12.0110
> 100 HC 1 STY HCH 17 0.003 1.0080
> 101 CR1 1 STY CCI 17 -0.016 12.0110
> 102 HC 1 STY HCI 17 0.003 1.0080
> 103 CR1 1 STY CCJ 17 -0.016 12.0110
> 104 HC 1 STY HCJ 17 0.003 1.0080
> 105 CH2 1 STY CCT 17 0.039 14.0270
> 106 CH1 1 STY CCS 18 0.060 13.0190
> 107 C 1 STY CCM 18 -0.027 12.0110
> 108 CR1 1 STY CCN 18 -0.018 12.0110
> 109 HC 1 STY HCN 18 0.001 1.0080
> 110 CR1 1 STY CCO 18 -0.018 12.0110
> 111 HC 1 STY HCO 18 0.002 1.0080
> 112 CR1 1 STY CCP 19 -0.016 12.0110
> 113 HC 1 STY HCP 19 0.003 1.0080
> 114 CR1 1 STY CCQ 19 -0.016 12.0110
> 115 HC 1 STY HCQ 19 0.003 1.0080
> 116 CR1 1 STY CCR 19 -0.016 12.0110
> 117 HC 1 STY HCR 19 0.003 1.0080
> 118 CH2 1 STY CDB 19 0.039 14.0270
> 119 CH2 1 STY CDA 20 0.066 14.0270
> 120 C 1 STY CCU 20 -0.019 12.0110
> 121 CR1 1 STY CCV 20 -0.012 12.0110
> 122 HC 1 STY HCV 20 0.003 1.0080
> 123 CR1 1 STY CCW 20 -0.013 12.0110
> 124 HC 1 STY HCW 20 0.004 1.0080
> 125 CR1 1 STY CCX 20 -0.013 12.0110
> 126 HC 1 STY HCX 20 0.004 1.0080
> 127 CR1 1 STY CCY 20 -0.013 12.0110
> 128 HC 1 STY HCY 20 0.003 1.0080
> 129 CR1 1 STY CCZ 20 -0.013 12.0110
> 130 HC 1 STY HCZ 20 0.003 1.0080
>
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 1 2 2 0.109 12300000.0 0.109 12300000.0 ; CAB HAB
> 1 3 2 0.139 10800000.0 0.139 10800000.0 ; CAB CAC
> .
> .
> .
> .
> .
> ************
>
> Thank you so much for your help :)
>
> Sincerely,
> Harshith, Under Graduate,
> IITK
> http://home.iitk.ac.in/~harshith
>
>
> ------------------------------------------------------------------------
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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