Thankyou David for your kind reply. I want to contruct a 5' protonatedphosphate sequence. So, I have followed the "sequence { OHE U CG }" (AMBER manual 21 section 3.2.3 "Some nonstandardsituations" page 45). Using “sequence {OHE U5 C G3}”,createsthe separate OH molecule molecule like :
ATOM 1 H OHE 1 1.866 1.500 -0.000 1.00 0.00
ATOM 2 O OHE 1 2.031 1.595 -0.941 1.00 0.00
TER
ATOM 3 HO5' U5 2 1.383 -5.568 1.469 1.00 0.00
ATOM 4 O5' U5 2 0.821 -4.791 1.434 1.00 0.00
ATOM 5 C5' U5 2 0.247 -4.401 0.173 1.00 0.00
ATOM 6 H5' U5 2 -0.379 -5.208 -0.208 1.00 0.00
ATOM 7 H5'' U5 2 1.044 -4.192 -0.541 1.00 0.00
ATOM 8 C4' U5 2 -0.603 -3.153 0.352 1.00 0.00
ATOM 9 H4' U5 2 -0.738 -2.663 -0.612 1.00 0.00
ATOM 10 O4' U5 2 -1.949 -3.552 0.752 1.00 0.00
ATOM 11 C1' U5 2 -2.129 -3.210 2.279 1.00 0.00
ATOM 12 H1' U5 2 -2.945 -2.496 2.390 1.00 0.00
ATOM 13 N1 U5 2 -2.618 -4.420 3.077 1.00 0.00
ATOM 14 C6 U5 2 -1.783 -5.414 3.514 1.00 0.00
ATOM 15 H6 U5 2 -0.726 -5.366 3.298 1.00 0.00
ATOM 16 C5 U5 2 -2.243 -6.431 4.256 1.00 0.00
ATOM 17 H5 U5 2 -1.561 -7.212 4.593 1.00 0.00
ATOM 18 C4 U5 2 -3.634 -6.509 4.618 1.00 0.00
ATOM 19 O4 U5 2 -4.145 -7.401 5.294 1.00 0.00
ATOM 20 N3 U5 2 -4.401 -5.467 4.137 1.00 0.00
ATOM 21 H3 U5 2 -5.462 -5.482 4.385 1.00 0.00
ATOM 22 C2 U5 2 -3.957 -4.408 3.371 1.00 0.00
ATOM 23 O2 U5 2 -4.714 -3.531 2.990 1.00 0.00
ATOM 24 C3' U5 2 -0.148 -2.191 1.452 1.00 0.00
ATOM 25 H3' U5 2 0.935 -2.303 1.498 1.00 0.00
ATOM 26 C2' U5 2 -0.779 -2.674 2.759 1.00 0.00
ATOM 27 H2' U5 2 0.007 -2.914 3.475 1.00 0.00
ATOM 28 O2' U5 2 -1.614 -1.645 3.295 1.00 0.00
ATOM 29 HO2' U5 2 -1.989 -1.984 4.111 1.00 0.00
ATOM 30 O3' U5 2 -0.504 -0.826 1.287 1.00 0.00
ATOM 31 P C 3 0.000 0.000 0.000 1.00 0.00
ATOM 32 OP1 C 3 1.480 0.000 0.000 1.00 0.00
ATOM 33 OP2 C 3 -0.678 1.316 0.000 1.00 0.00
ATOM 34 O5' C 3 -0.426 -0.903 -1.250 1.00 0.00
Thanks and Regards,
Saikat Pal
On Thursday, 21 October, 2021, 2:17:46 pm GMT-4, David A Case <david.case.rutgers.edu> wrote:
On Thu, Oct 21, 2021, Saikat Pal wrote:
>I have generated a RNA sequence in tleap using the following command:source
>leaprc.RNA.ROC
>m = sequence {OHE U C G}
What you wnat here is sequence { U5 C G3 }. This will "cap" the 5' and 3'
ends of the sequence in the intended way. Try that, and see if you get what
you want.
[Aside 1: when reading PDB files, tleap by default makes the first
nucleotide a 5' version, and the final nucleotide is made a 3' variant. But
this default doesn't persist into the "sequence" command: there you have to
specify the "5" and "3" labels specifically.]
[Aside 2: the three-dimensional structure you will get by just using a
sequence command may not be what you want. A general alternative is to use
a different program to create a three-dimensional structure, and then just
read that into tleap. (Amber's NAB is one such program, but probably not
the best one for most people today.) Remember that tleap is a very "dumb"
program -- it primarily does bookkeeping. Don't expect it to actually know
anything about RNA.]
....dac
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Received on Thu Oct 21 2021 - 13:00:02 PDT
