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.

Additional common options