AMBER Archive (2009)

Subject: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Nov 04 2009 - 06:17:53 CST

On Wed, Nov 04, 2009, zgong.hust wrote:
>
> I would like to simulate the RNA with one seperate Adenine molecule. The end of the PDB file is like this
>
....
> ATOM 1496 C2 G X 83 2.629 2.186 -2.432 1.00 89.50 C
> ATOM 1497 N2 G X 83 2.185 1.128 -3.130 1.00 89.30 N
> ATOM 1498 N3 G X 83 3.069 3.273 -3.071 1.00 89.41 N
> ATOM 1499 C4 G X 83 3.479 4.245 -2.208 1.00 89.41 C
> TER 1500 G X 83
> HETATM 1506 N9 ADE X 90 18.599 -19.496 5.363 1.00 36.40 N
> HETATM 1507 C8 ADE X 90 19.317 -18.826 6.330 1.00 37.43 C
> HETATM 1508 N7 ADE X 90 19.960 -17.765 5.878 1.00 37.14 N
> HETATM 1509 C5 ADE X 90 19.606 -17.738 4.549 1.00 37.42 C
> HETATM 1510 C6 ADE X 90 19.944 -16.854 3.520 1.00 37.76 C
> HETATM 1511 N6 ADE X 90 20.739 -15.818 3.734 1.00 36.15 N
> HETATM 1512 N1 ADE X 90 19.447 -17.084 2.287 1.00 36.86 N
> HETATM 1513 C2 ADE X 90 18.651 -18.139 2.096 1.00 37.35 C
> HETATM 1514 N3 ADE X 90 18.270 -19.058 2.981 1.00 38.33 N
> HETATM 1515 C4 ADE X 90 18.784 -18.792 4.203 1.00 37.55 C
>
> There are ten Adenine atoms at the end of the pdb file
>
> When I use the tleap with leap.rna.ff98 force field, some errors happened
>
> > model=loadpdb 1y26_1.pdb
> Loading PDB file: ./1y26_1.pdb
> Added missing heavy atom: .R<RA3 84>.A<C1' 11>
> Added missing heavy atom: .R<RA3 84>.A<O4' 10>

In the Amber library, "ADE" means adenosine (the nucleotide), not just the
base. It's probably easiest to rename the ADE part to something else, and to
create a unit that just has those atoms.

...dac

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