We solved the RNA structure using NMR. we would like to refine the structure using Gromacs or amber. does anyone know that how to convert the xplor distance restraints/dihedral to Gromacs (disre.itp) or amber format for RNA ?
Thanking you.
You may find this helpful:
NAME
xplor2gmx - Convert XPLOR distance restraints to Gromacs format
SYNOPSIS
xplor2gmx (residue offset) input.pdb
DESCRIPTION
xplor2gmx reads an XPLOR input file with distance restraint data as
sometimes is found in the pdb database (http://www.pdb.org ). From this
input file dihedral restrints should be removed, such that only
distance restraints are left. The script can handle ambiguous
restraints. It converts the distance restraints to GROMACS format.
A restraints file (.dat) should be provided on STDIN, and a suitable
output file (.itp) is sent to STDOUT.
EXAMPLES
xplor2gmx.pl 33 conf.pdb < restraints.dat > disre.itp
OPTIONS
xplor2gmx requires two command line options: first, the residue offset
(integer); second, the .pdb filename. The pdb file must have correct
atom numbers.
Reference:
http://manpages.ubuntu.com/manpages/utopic/man1/xplor2gmx.1.html
Dear John Anyam,
Thanks for your reply. i will try to work on it :-)
Looks like this command works only works for protein not for RNA/DNA.
it is showing following error :
Can not open atom-name translation table /usr/local/gromacs-5.0.4/share/gromacs/gromacs/top/atom_nom.tbl
Then i checked the atom_nom.tbl
vi atom_nom.tbl
# Correlation of hydrogen atom naming systems, including diastereotopic
# protons. The original version of this table was created by Charles
# Hoogstraten.
#
# BMRB = System in use at BioMagResBank (IUPAC/IUB Biochemistry 9, 3471-3479
# [1970]).
#
# SC = Stereochemical designations
#
# UCSF = Mardigras-type software (peptide protonated with newhyd utility).
#
# XPLOR = Peptide protonated with XPLOR 3.1. Atom nomenclature is derived
# from the X-PLOR topology file topallhdg.pro.
#
# MSI = Artificial peptide created with InsightII. For the side chain
# protons attached to nitrogen in ASN, GLN, and ARG, the atom
# nomenclature does not reflect the potential stereoisomerism of the
# planar amide and guanidinium groups. The correlation with Z and E
# nomenclature listed here simply reflects the state of the artificial
# peptide generated as an example. The CG1 and CG2 atoms for VAL in a
# peptide generated by InsightII are not labeled according to IUPAC
# rules, while the CD1 and CD2 atoms for LEU are.
#
"atom_nom.tbl" [readonly] 407L, 8016C
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