AMBER: build RNA by nucgen

From: 欧阳德方 <ouyangdf1978.hotmail.com>
Date: Sun, 13 Jan 2008 10:26:44 +0800

Hi, all,

I want to build RNA by nucgen.
The sequence of RNA have 21 residues :
5'-GCAACAGUUACUGCGACGUUU-3'
3'-UUCGUUGUCAAUGACGCUGCA-5'

The rna_nuc.in:
  NUC 1
R
G5 C A A C A G U U A C U G C G A C G U U U3

  NUC 2
R
A5 C G U C G C A G U A A C U G U U G C U U3

END
$ARNA
 
The command is:
nucgen -O -i rna_nuc.in -o rna_nuc.out -d $AMBERHOME/dat/leap/parm/nucgen.dat -p rna_nuc.pdb

But the output file rna_nuc.out is:
          Amber 5 NUCGEN UCSF 1997
          ------------------------------------------------------

               INPUT MOLECULES INFORMATION

  NUC 1

     MOLECULE 1 CONTAINS 16 RESIDUES:

     G5 C A A C A G U U A C U
G C G A
  NUC 2

     MOLECULE 2 CONTAINS 16 RESIDUES:

     A5 C G U C G C A G U A A
C U G U
    New (1994) residue naming convention

          GENERATING RIGHT HANDED A-RNA(ARNOTT)

  reading monomer parameters

It shows only 16 residues for each chain and the output file rna_nuc.pdb is also shown only 16 residues for each chain. It lost the last 5 residues of each chain.
ATOM 1 H5T G5 1 2.907 -8.210 3.750
ATOM 2 O3' G5 1 7.297 -6.145 5.250
ATOM 3 O5' G5 1 4.232 -7.360 3.480
---
ATOM    739  C2  U      32       6.596  -0.670  -3.850
ATOM    740  O2  U      32       7.266  -1.691  -3.850
ATOM    741  N1  U      32       7.098   0.559  -4.200
ATOM    742  C6  U      32       6.317   1.693  -4.190
ATOM    743  C5  U      32       5.019   1.640  -3.850
I cannot find the reason why it makes mistake.
Could u help me?
Thanks a lot!
Ouyang Defang
School of Pharmacy
University of Queensland
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Received on Sun Jan 13 2008 - 06:07:39 PST
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