AMBER Archive (2009)

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

From: zgong.hust (zgong.hust_at_gmail.com)
Date: Wed Nov 04 2009 - 06:59:20 CST

Dear sir
      Could you please tell me in detail how can I create a unit that just has these atoms ?
I have change the name of ADE to "SOL", however, the errors still exsit

PDB file:

ATOM 1493 C6 G X 83 3.005 3.061 -0.159 1.00 89.27 C
ATOM 1494 O6 G X 83 2.942 2.890 1.064 1.00 89.30 O
ATOM 1495 N1 G X 83 2.590 2.068 -1.054 1.00 89.82 N
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 SOL X 90 18.599 -19.496 5.363 1.00 36.40 N
HETATM 1507 C8 SOL X 90 19.317 -18.826 6.330 1.00 37.43 C
HETATM 1508 N7 SOL X 90 19.960 -17.765 5.878 1.00 37.14 N
HETATM 1509 C5 SOL X 90 19.606 -17.738 4.549 1.00 37.42 C
HETATM 1510 C6 SOL X 90 19.944 -16.854 3.520 1.00 37.76 C
HETATM 1511 N6 SOL X 90 20.739 -15.818 3.734 1.00 36.15 N
HETATM 1512 N1 SOL X 90 19.447 -17.084 2.287 1.00 36.86 N
HETATM 1513 C2 SOL X 90 18.651 -18.139 2.096 1.00 37.35 C
HETATM 1514 N3 SOL X 90 18.270 -19.058 2.981 1.00 38.33 N
HETATM 1515 C4 SOL X 90 18.784 -18.792 4.203 1.00 37.55 C

tleap output

> model=loadpdb 1y26_a.pdb
Loading PDB file: ./1y26_a.pdb
Unknown residue: SOL number: 71 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: SOL sequence: 84
Created a new atom named: N9 within residue: .R<SOL 84>
Created a new atom named: C8 within residue: .R<SOL 84>
Created a new atom named: N7 within residue: .R<SOL 84>
Created a new atom named: C5 within residue: .R<SOL 84>
Created a new atom named: C6 within residue: .R<SOL 84>
Created a new atom named: N6 within residue: .R<SOL 84>
Created a new atom named: N1 within residue: .R<SOL 84>
Created a new atom named: C2 within residue: .R<SOL 84>
Created a new atom named: N3 within residue: .R<SOL 84>
Created a new atom named: C4 within residue: .R<SOL 84>
  total atoms in file: 1509
  Leap added 758 missing atoms according to residue templates:
       758 H / lone pairs
  The file contained 10 atoms not in residue templates

Thank you very much


2009-11-04



Zhou Gong
School of Physics
Huazhong University of Science and Technology
Wuhan
Hubei Province
China



发件人： case
发送时间： 2009-11-04 20:19:30
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] errors on leap for a RNA+Adenine pdb structure
 
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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