AMBER Archive (2009)

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

From: zgong.hust (zgong.hust_at_gmail.com)
Date: Wed Nov 04 2009 - 00:18:41 CST

Dear Amber Users:

       I would like to simulate the RNA with one seperate Adenine molecule. The end of the PDB file is like this

ATOM 1486 C2' G X 83 2.960 6.532 -4.618 1.00 89.15 C
ATOM 1487 O2' G X 83 3.226 6.631 -6.010 1.00 88.10 O
ATOM 1488 C1' G X 83 4.216 6.065 -3.876 1.00 89.43 C
ATOM 1489 N9 G X 83 3.991 5.487 -2.537 1.00 89.66 N
ATOM 1490 C8 G X 83 4.252 6.089 -1.327 1.00 89.52 C
ATOM 1491 N7 G X 83 3.957 5.376 -0.282 1.00 89.03 N
ATOM 1492 C5 G X 83 3.473 4.208 -0.827 1.00 89.02 C
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 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>
  Added missing heavy atom: .R<RA3 84>.A<C2' 29>
  Added missing heavy atom: .R<RA3 84>.A<C4' 8>
  Added missing heavy atom: .R<RA3 84>.A<C3' 27>
  Added missing heavy atom: .R<RA3 84>.A<O2' 31>
  Added missing heavy atom: .R<RA3 84>.A<C5' 5>
  Added missing heavy atom: .R<RA3 84>.A<O3' 33>
  Added missing heavy atom: .R<RA3 84>.A<O5' 4>
  Added missing heavy atom: .R<RA3 84>.A<P 1>
  Added missing heavy atom: .R<RA3 84>.A<O1P 2>
  Added missing heavy atom: .R<RA3 84>.A<O2P 3>
  total atoms in file: 1509
  Leap added 782 missing atoms according to residue templates:
       12 Heavy
       770 H / lone pairs
>

It adds many extral atoms what I don't want, and I couldn't save the top and crd files

Please help me out!

Thanks for your patient and help

2009-11-04

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