Usage:
nucgen [-O] -i ngin -o ngout -d ngdat -p pdbout
This program generates cartesian coordinate models for either double helical DNA or RNA with a number of possible conformations. The helical topology of the double helix is stored in a file for individual types in terms of cylindrical coordinates. The program loads the required topoplogy and applies two fold symmetry with necessary helical repeat and height values. The cartesian coordinates are output in PDB format. The residue information is read as in the link module either for DNA or RNA. The input is described below.
NUCGEN requires specification of two strands: if only one is given, it will wrap it into two with highly stretched base-phosphate bonds across the end, so for single strands, specify a dummy strand and edit it out of the resulting PDB file. NUCGEN only generates reasonable geometries for complementary base pairs.
NUCGEN can generate PDB files using the 1994 Amber force field convention, which does not have explicit terminal hydrogen or phosphate residues. For the new residue names, only the bases need to be specified, while for the old convention, terminal hydrogen residues (HB and HE) and phosphates (POM) must also be specified. In the 1994 convention, residues are indicated by the first letter (A, G, C, T) and terminal residues have an additional 5 or 3 appended (e.g. A5, A3). See the LINK documentation for a table of these names. The residue names in the input file must all be of either the old or the new convention - mixed conventions will not work.
On VMS systems files are assigned by Fortran unit number. These are given below along with a description of each file.
ngin 5 Input: Control and sequence data for the run
ngout 6 Output: Diagnostics
ngdat 7 Input: Monomer geometry file, found in amber41/dat
pdbout 10 Output: PDB output coordinates
Nucleic Acid sequence information is given as described here for each strand. Both strands are entered in the 5' to 3' direction. This input is similar to LINK.
- 1A - A TITLE FOR EACH STRAND
FORMAT(20A4)
TITLE A title for the molecule.
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- 1B - ILBMOL
FORMAT(A4)
ILBMOL Label for the type of molecule.
'D' DNA
'R' RNA
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- 1C - RESIDUE INFORMATION FOR EACH STRAND
it is read in the following format until a blank
card is encounterd (card 1D).
LBRES(I) , I = 1,NRESM
FORMAT(16(A4,1X))
LBRES(I) Residue name.
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- 1D - Blank Card to terminate residue input
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NOTE: Cards 1A-1D are repeated for the second strand.
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- 2 - KEND
FORMAT(A4)
KEND Control to stop reading the nucleotide strands.
'END ' end of reading the sequence information
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- 3 - CONTROL FOR THE TYPE OF DNA OR RNA CONFORMATION
TYPM
FORMAT(A8)
TYPM Name of the type of conformation to be generated.
'$ARNA' right handed a-rna (arnott)
'$APRNA' right handed a-prime rna (arnott)
'$LBDNA' right handed bdna (langridge)
'$ABDNA' right handed bdna (arnott)
'$SBDNA' left handed bdna (sasisekharan)
'$ADNA' right handed a-dna (arnott)
'$SPECIAL' special type by the user
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- 4 - special helical parameter
***** only if typm .eq. '$SPECIAL' *****
hxrep , hxht
format(2f10.5)
hxrep Helical repeat angle in degrees for the special
type of conformation.
hxht Helical height.
NOTE: If you use '$SPECIAL', you will have to
add the appropriate data to file ngdat (found
in the database directory). Consult subroutine
gennuc for details.
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