Hello Zhonghe--
>
> 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.
That sounds like a good plan.
>
> corresponding, I also prepared the topology and the parameter files
> for the novel monatomic molecule (nitroxide oxygen) as bellowing:
>
>
> 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
This indicates that there is a nonstandard residue type, which is
true, and it means that you will need to either generate PSF info some
other way - like you tried.
> 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 is quite difficult to manipulate a PSF file by hand- I recommend
against it. Instead, you can generate a .psf file from a topology file
- you can see examples in the eginput/PSF_generate directory in the
Xplor-NIH distribution.
If your residue truly has only a single atom, and you use only
RepelPot for nonbonded interactions, you will not need any parameters
- simply leave these atoms out of your selection.
Charles
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