Dear All,
I have realized something while using nucgen. I tried to create an A-form
RNA of 5'GGCC3'. According to the manual (pp.237), nucgen uses the 94
convention for residue names. In pp.48, the residue naming for 94 force
field is saying that the "R" prefix should be used for RNA's. In any case,
I have created the following nucgen input file:
---------------- ggcc_nuc_mod.in ------------------------
Strand # 1 - GGCC
R
RG5 RG RC RC3
Strand # 2 - GGCC
R
RG5 RG RC RC3
END
$ARNA
--------------------------------------------------------
After running nucgen;
nucgen -O -i ggcc_nuc_mod.in -o ggcc_nuc_mod.out -d
$AMBERHOME/dat/leap/parm/nucgen.dat -p ggcc_nuc_mod.pdb
it created the following .out file:
---------------------- ggcc_nuc_mod.out -----------------------
------------------------------------------------------
Amber 5 NUCGEN UCSF 1997
------------------------------------------------------
INPUT MOLECULES INFORMATION
Strand # 1 - GGCC
MOLECULE 1 CONTAINS 4 RESIDUES:
RG5 RG RC RC3
Strand # 2 - GGCC
MOLECULE 2 CONTAINS 4 RESIDUES:
RG5 RG RC RC3
Unknown residue: RG5
Unknown residue: RG
Unknown residue: RC
Unknown residue: RC3
Unknown residue: RG5
Unknown residue: RG
Unknown residue: RC
Unknown residue: RC3
RESIDUE NAMES ARE NOT UNIFORMLY OLD OR 1994 NUCLEIC ACIDS
-------------------------------------------------------------
So, it seems that nucgen is not using the 94 convention. Then I have
changed the nucgen input file as following, to see what will happen:
----------------------- ggcc_nuc.in -------------------------------
Strand # 1 - GGCC
R
G5 G C C3
Strand # 2 - GGCC
R
G5 G C C3
END
$ARNA
-------------------------------------------------------------------
After running nucgen, I did not encounter any problem, except that the
naming of the residues in the .pdb file are not RG or RC but G or C (which
means DNA). As an example, I am including some part of the .pdb file:
-------------------------------------------------------------------
....
ATOM 21 N3 G5 1 6.848 -2.225 0.940
ATOM 22 C2 G5 1 6.597 -0.986 0.550
ATOM 23 N1 G5 1 5.325 -0.513 0.260
ATOM 24 H1 G5 1 5.202 0.438 -0.030
ATOM 25 P G 2 6.882 -5.338 6.560
ATOM 26 O1P G 2 7.505 -5.970 7.750
ATOM 27 O2P G 2 5.404 -5.201 6.610
ATOM 28 O3' G 2 9.461 -1.229 8.060
ATOM 29 O5' G 2 7.538 -3.907 6.290
ATOM 30 C1' G 2 8.527 -0.626 4.580
....
-------------------------------------------------------------------
When I open this .pdb file in xleap, and edit it, I see that it is not an
RNA but a DNA. (Prob. because of the residue naming, when a ff is called
in xleap, it will see it as a DNA residue)
Is there any bugfix for that? Thanks in advance.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
---------------------------------------------------------------
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Received on Sat Feb 12 2005 - 01:53:00 PST
