[gmx-users] Fatal error:Atom index (1) in settles out of bounds (1-0)
Yang Ye
leafyoung at yahoo.com
Mon Nov 5 08:29:01 CET 2007
Hi,
To use GROMACS' spc topology with ffamber, you may create a new spc
topology, e.g. spc-amber.itp. Following is its content. If you know C
preprocessor, you can merge it with original spc.itp.
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 amber99_54 1 SOL OW 1 -0.82 15.99940
2 amber99_55 1 SOL HW1 1 0.41 1.00800
3 amber99_55 1 SOL HW2 1 0.41 1.00800
#ifdef FLEXIBLE
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
#else
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16333
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
On 11/5/2007 2:59 PM, willting wrote:
> Hi,
> I added ffamber_v3.3.1 to gromacs-3.3.1 and wanted to use the
> AMBER99 Wang protein/nucleic acid forcefield.
> Run the commands:
> pdb2gmx -ignh -f sev.pdb -o sev.gro -p sev.top -missing -water spc
> editconf -bt cubic -f sev.gro -o sev_box.gro -c -d 1
> genbox -cp sev_box.gro -cs -p sev.top -o sev_water.gro
> grompp -v -f em.mdp -c sev.gro -p sev.top -o sev_em.tpr
>
> then it showed:
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: toppush.c, line: 1108
>
> Fatal error:
> [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
> Atom index (1) in settles out of bounds (1-0)
> -------------------------------------------------------
> what should I do ?
>
> Thanks,
>
> will
>
> * My pdb:
> ATOM 3072 N NPHE P 1 49.900 57.324 4.858 1.00 17.05 N
> ATOM 3073 CA NPHE P 1 49.015 58.449 4.532 1.00 17.68 C
> ATOM 3074 C NPHE P 1 48.529 58.242 3.088 1.00 17.14 C
> ATOM 3075 O NPHE P 1 49.336 58.259 2.133 1.00 18.44 O
> ATOM 3076 CB NPHE P 1 49.786 59.754 4.742 1.00 1850 C
> ATOM 3077 CG NPHE P 1 48.955 60.964 4.622 1.00 22.19 C
> ATOM 3078 CD1 NPHE P 1 48.146 61.341 5.652 1.00 28.37 C
> ATOM 3079 CD2 NPHE P 1 48.962 61.710 3.451 1.00 30.13 C
> ATOM 3080 CE1 NPHE P 1 47.364 62.498 5.562 1.00 33.16 C
> ATOM 3081 CE2 NPHE P 1 48.231 62.874 3.360 1.00 31.49 C
> ATOM 3082 CZ NPHE P 1 47.415 63.254 4.420 1.00 33.03 C
> ATOM 3083 N ALA P 2 47.231 57.937 3.024 1.00 17.87 N
> ATOM 3084 CA ALA P 2 46.514 57.524 1.824 1.00 18.82 C
> ATOM 3085 C ALA P 2 46.531 58.561 0.717 1.00 19.39 C
> ATOM 3086 O ALA P 2 46.622 59.753 0.962 1.00 18.85 O
> ATOM 3087 CB ALA P 2 45.082 57.093 2.184 1.00 18.07 C
> ATOM 3088 N PRO P 3 46.475 58.093 -0.513 1.00 20.13 N
> ATOM 3089 CA PRO P 3 46.273 59.006 -1.620 1.00 23.52 C
> ATOM 3090 C PRO P 3 44.935 59.714 -1.371 1.00 26.20 C
> ATOM 3091 O PRO P 3 43.968 59.104 -0.883 1.00 30.44 O
> ATOM 3092 CB PRO P 3 46.123 58.061 -2.834 1.00 22.88 C
> ATOM 3093 CG PRO P 3 46.724 56.802 -2.456 1.00 20.87 C
> ATOM 3094 CD PRO P 3 46.550 56.684 -0.930 1.00 18.82 C
> ATOM 3095 N GLY P 4 44.860 60.944 -1.765 1.00 30.11 N
> ATOM 3096 CA GLY P 4 43.552 61.581 -1.771 1.00 32.23 C
> ATOM 3097 C GLY P 4 43.266 61.997 -3.211 1.00 30.90 C
> ATOM 3098 O GLY P 4 44.171 62.226 -3.966 1.00 34.59 O
> ATOM 3099 N ASN P 5 42.016 62.091 -3.590 1.00 33.27 N
> ATOM 3100 CA ASN P 5 41.666 62.673 -4.864 1.00 32.62 C
> ATOM 3101 C ASN P 5 41.960 61.777 -6.056 1.00 31.39 C
> ATOM 3102 O ASN P 5 42.610 62.291 -6.989 1.00 33.62 O
> ATOM 3103 CB ASN P 5 42.445 63.999 -5.073 1.00 35.10 C
> ATOM 3104 CG ASN P 5 42.229 65.016 -3.907 1.00 40.06 C
> ATOM 3105 OD1 ASN P 5 41.098 65.202 -3.404 1.00 47.96 O
> ATOM 3106 ND2 ASN P 5 43.323 65.656 -3.468 1.00 47.14 N
> ATOM 3107 N TYR P 6 41.551 60.487 -6.012 1.00 24.72 N
> ATOM 3108 CA TYR P 6 41.616 59.590 -7.164 1.00 22.15 C
> ATOM 3109 C TYR P 6 40774 60.234 -8.266 1.00 21.95 C
> ATOM 3110 O TYR P 6 39.555 60.176 -8.207 1.00 21.25 O
> ATOM 3111 CB TYR P 6 41.068 58.202 -6.866 1.00 21.39 C
> ATOM 3112 CG TYR P 6 41.847 57.366 -5.863 1.00 19.06 C
> ATOM 3113 CD1 TYR P 6 41.589 57.466 -4.512 1.00 16.12 C
> ATOM 3114 CD2 TYR P 6 42.800 56.441 -6.274 1.00 15.31 C
> ATOM 3115 CE1 TYR P 6 42.257 56.717 -3.628 1.00 15.10 C
> ATOM 3116 CE2 TYR P 6 43.510 55.696 -5.390 1.00 13.45 C
> ATOM 3117 CZ TYR P 6 43.226 55.805 -4.054 1.00 15.29 C
> ATOM 3118 OH TYR P 6 43.914 55.071 -3.133 1.00 14.56 O
> ATOM 3119 N PRO P 7 41.417 60.776 -9.285 1.00 21.63 N
> ATOM 3120 CA PRO P 7 40.708 61.437 -10.395 1.00 21.38 C
> ATOM 3121 C PRO P 7 39.731 60.470 -11.044 1.00 20.08 C
> ATOM 3122 O PRO P 7 40.005 59.287 -11.207 1.00 18.00 O
> ATOM 3123 CB PRO P 7 41.824 61.799 -11.375 1.00 23.11 C
> ATOM 3124 CG PRO P 7 43.064 61.687 -10.604 1.00 25.67 C
> ATOM 3125 CD PRO P 7 42.862 60.695 -9.527 1.00 23.44 C
> ATOM 3126 N ALA P 8 38.590 60.992 -11.468 1.00 18.89 N
> ATOM 3127 CA ALA P 8 37.595 60.159 -12.075 1.00 18.81 C
> ATOM 3128 C ALA P 8 38.061 59.569 -13.390 1.00 17.43 C
> ATOM 3129 O ALA P 8 38.796 60.195 -14.168 1.00 18.08 O
> ATOM 3130 CB ALA P 8 36.306 60.943 -12.286 1.00 19.45 C
> ATOM 3131 N CLEU P 9 37.637 58.345 -13.643 1.00 16.96 N
> ATOM 3132 CA CLEU P 9 37.959 57.644 -14.866 1.00 18.11 C
> ATOM 3133 C CLEU P 9 37.229 58.236 -16.066 1.00 18.76 C
> ATOM 3134 OC1 CLEU P 9 36.273 59.002 -15.893 1.00 19.22 O
> ATOM 3135 CB CLEU P 9 37.536 56.180 -14.732 1.00 18.89 C
> ATOM 3136 CG CLEU P 9 38.185 55.363 -13.653 1.00 19.67 C
> ATOM 3137 CD1 CLEU P 9 37.635 53.964 -13.635 1.00 21.54 C
> ATOM 3138 CD2 CLEU P 9 39.637 55.309 -13.857 1.00 20.00 C
> ATOM 3139 OC2 CLEU P 9 37.619 57.946 -17.224 1.00 17.47 O
> TER 3140 LEU P 9
>
>
>
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