seq2psf
Generate a PSF file from a PDB file. This is only possible for PDBs with residues contained in Xplor-NIH's default topology database.
Usage: seq2psf [-protein | -dna | -rna] [option] <sequence filename>
Option is one or more of:
-outFile <filename> -segname <segment name> -startresid <lowest residue number> -cisPeptide resid -disulfide_bond resid1:resid2 -disulfide_bridge resid1:resid2 -protonateHIS -deprotonateHIS resid1[:resid2...] -amidate_cterm -custom_rename -singleChar
If the sequence type is omitted, a guess is made- this will not work correctly for rna sequences- you must specify -rna.
generates a psf file from protein or nucleic acid sequence the psf file is written in a filename derived the input filename.
multiple chains (not covalently linked) can be obtained by using the special residue name '*'.
The -cisPeptide N option specifies that there is a cis peptide bond between residues N and N+1.
use -disulfide_bond to make actual bonds, and -disulfide_bridge to remove the cysteine HG proton- to form disulfide with an NOE restraint.
use -amidate_cterm to terminate the c-terminal end with a CONH2 group.
By default the HIS HD1 atom is deleted. If -protonateHIS is specified, this proton is not deleted. Alternately, the resids of all residues which should be deprotonated can be specified using the -deprotonateHIS option, with resids specified, separated by colons. Finally, residue name variants can be used to specify protonation state: HIS (fully protonated), HSD (HD1 present, no HE2), and HSE (HE2 present, no HD1). If HSD or HSE is present, the -protonateHIS and -depronateHIS flags are ignored.
If -outFile is omitted, the output filename is that of the input file with its suffix replaced with .psf.
If -custom_rename is specified, certain convenient atom renamings are made for nucleic acids:
ADE H61 --> HN' ADE H62 --> HN'' GUA H21 --> HN' GUA H22 --> HN'' CYT H41 --> HN' CYT H42 --> HN'' THY C5A --> CM
The -singleChar option should be used for an input filename containing sequence information in single-character format. By default, residues are specified by the full 3 residue (or 4, for modified residues) name.
Example:
% seq2psf -segname PROT -startresid 300 -protein protG.seq
creates protG.psf with segid PROT starting with residue id 300.