I think it depends on the version of force field you are using. For example,
if you are using ff03, RNAs are formatted as RA, RG, etc. However if you are
using ff10, which employed a different pdb format, RNAs are now A, G, etc.
So yo probably wanna go check those parameter files and figure out how RNA
atoms/residues were defined.
Hope this helps.
Victor
On Mon, Oct 3, 2011 at 9:26 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> Dear users,
>
> I am new to Amber. I am trying to generate prmtop and inpcrd files by using
> saveamberparm but getting this error message again and again:
>
> FATAL: Atom .R<RG5 1>.A<H02' 33> does not have a type.
> FATAL: Atom .R<RG 2>.A<H02' 35> does not have a type.
> FATAL: Atom .R<RG 3>.A<H02' 35> does not have a type.
> FATAL: Atom .R<RA 4>.A<H02' 34> does not have a type.
> FATAL: Atom .R<RA 5>.A<H02' 34> does not have a type.
> FATAL: Atom .R<RG 6>.A<H02' 35> does not have a type.
>
> I guess something is wrong with the PDB file. Can anyone suggest what all
> modifications are required in an RNA PDB file. A sample of my file is also
> attached. I have removed 5' terminal phosphate.
>
> ATOM 4 O5' G A 1 1.593 0.000 0.000 1.00 0.00
>
> ATOM 5 C5' G A 1 2.329 1.239 0.000 1.00 0.00
>
> ATOM 6 C4' G A 1 3.773 0.965 0.348 1.00 0.00
>
> ATOM 7 O4' G A 1 3.857 0.543 1.736 1.00 0.00
>
> ATOM 8 C3' G A 1 4.428 -0.164 -0.432 1.00 0.00
>
> ATOM 9 O3' G A 1 4.939 0.287 -1.690 1.00 0.00
>
> ATOM 10 C1' G A 1 4.847 -0.474 1.873 1.00 0.00
>
> ATOM 11 C2' G A 1 5.537 -0.609 0.515 1.00 0.00
>
> ATOM 12 O2' G A 1 6.671 0.234 0.469 1.00 0.00
>
> ATOM 13 N1 G A 1 4.670 -5.266 3.516 1.00 0.00
>
> ATOM 14 C2 G A 1 5.758 -4.483 3.215 1.00 0.00
>
> ATOM 15 N2 G A 1 6.960 -5.051 3.390 1.00 0.00
>
> ATOM 16 N3 G A 1 5.674 -3.238 2.778 1.00 0.00
>
> ATOM 17 C4 G A 1 4.393 -2.828 2.663 1.00 0.00
>
> ATOM 18 C5 G A 1 3.239 -3.529 2.935 1.00 0.00
>
> ATOM 19 C6 G A 1 3.343 -4.865 3.401 1.00 0.00
>
> ATOM 20 O6 G A 1 2.434 -5.651 3.699 1.00 0.00
>
> ATOM 21 N7 G A 1 2.118 -2.749 2.684 1.00 0.00
>
> ATOM 22 C8 G A 1 2.604 -1.610 2.271 1.00 0.00
>
> ATOM 23 N9 G A 1 3.976 -1.591 2.236 1.00 0.00
>
> ATOM 24 1H5* G A 1 1.891 1.938 0.726 1.00 0.00
>
> ATOM 25 2H5* G A 1 2.262 1.717 -0.988 1.00 0.00
>
> ATOM 26 H4' G A 1 4.289 1.907 0.114 1.00 0.00
>
> ATOM 27 H3' G A 1 3.736 -0.975 -0.704 1.00 0.00
>
> ATOM 28 H1' G A 1 5.640 -0.463 2.635 1.00 0.00
>
> ATOM 29 H2' G A 1 5.924 -1.609 0.274 1.00 0.00
>
> ATOM 30 H02' G A 1 7.502 -0.321 0.511 1.00 0.00
>
> ATOM 31 H1 G A 1 4.845 -6.195 3.841 1.00 0.00
>
> ATOM 32 1H2 G A 1 7.792 -4.532 3.191 1.00 0.00
>
> ATOM 33 2H2 G A 1 7.025 -5.992 3.720 1.00 0.00
>
> ATOM 34 H8 G A 1 1.976 -0.753 1.981 1.00 0.00
>
>
> Thanks,
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>
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Received on Mon Oct 03 2011 - 08:30:03 PDT
