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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Received on Mon Oct 03 2011 - 07:30:04 PDT
