Hi Xplor-nih users:
I want to do rigid-body modeling for biopolymer with distance-restraint from
EPR experiment. following the previous work (Norman et al, 2014, methods; Clore
et al, 2019, PNAS), I firstly generated set of nitroxide spin conformers for
each labeled site. second, only the nitroxide oxygen atoms of spin conformers
for each labeled site were reserved and grouped into segment with segid
identical to resid of labeled site. The segment will be treated as rigid-body
with its corresponding domain, And the averaged value of all pair between two
segments will be used for distance-restraint modeling.
corresponding, I also prepared the topology and the parameter files for the
novel monatomic molecule (nitroxide oxygen) as bellowing:
!----------------------------------------------------
remarks file toppar/SPIN.top
set echo on end
autogenerate angles=true end
MASS OV 16.00
!------------------------------------------------------------------
RESIdue SPIN
GROUp
ATOM OV TYPE=OV CHARGE=0.0 END
END {SPIN}
set echo=on end
!----------------------------------------------------
remarks file name: toppar/SPIN.par
remarks
set echo off end
NONBonded OV 0.1600 3.00 0.1600 3.00
nbfix OV OV 0.0000 0.0 0.0000 0.00
set echo=on end
-------------------------------------------------------
Then, I run script using xplor-nih 3.2 on PDB (SPIN.pdb) file containing single
SPIN atom. The script is :
##########
protocol.initTopology("SPIN.top")
protocol.initParams("SPIN.par")
protocol.loadPDB('SPIN.pdb') # "ATOM 6721 OV SPIN 1 35.014 8.744
-4.057 1.00 0.00 186"
print(len(AtomSel("ALL")))
print(len(AtomSel("not known")))
print(len(AtomSel("known")))
#################
I got error message:
"loading pdb file: SPIN.pdb seqToPSF: Warning: unsupported sequence type:
unknown: SPIN
[psf] PDBTool:read: atom not found in structure: 186 SPIN 1 OV
matchInexactAtomEntry: found no match for entry 186 1 OV
initCoords: Warning: unable to read 1 pdb ATOM entries (nonpseudoatom)"
alternative, I also tried to add the SPIN information in original PSF for
biopolymer in the corresponding section, i.e NATOM , and NGRP, using home-made
script. when xplor-nih read the PSF file. it also reported error:
----------------------------
STRUcture> 17 0 0 20 0 0 24 0
0
%STRUcture-ERR: unrecognized command:
17
^^
-----------------------------
it appeared that the program encounter error when it reads the information from
section of NGRP (last section).
Thank in advance for any suggestion.
Best Regards
Zhonghe Xu
########################################################################
To unsubscribe from the XPLOR-NIH list, click the following link:
http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
