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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