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
_________________________________________________________________
天凉了，添衣了，心动了，“七件”了
http://get.live.cn
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jan 13 2008 - 06:07:39 PST
