[Xplor-nih] seq2psf topology file

[Charles at Schwieters.org]

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Hello--

> I would like to use seq2psf to create a protein that contains
> hydroxyproline (HYP). Which topology file does seq2psf use? Is there a
> standard topology and paramater file that already has HYP or do I need
> to add it? 

One approach would be to add HYP to toppar/protein.top and associated
parameters to toppar/protein.par. You would also need to add HYP
residueTypes['prot'] at the top of python/psfGen.py.

Alternatively, you could follow the example in
eginput/PSF_generation/addAtoms.py
replacing CYSP (MTSL) with HYP. This is probably an easier route to get
a psf. If you're not not working from a homologous protein (you have no
starting structure), you can replace the lines

protocol.addUnknownAtoms(dyn_stepsize=0.01)
protocol.fixupCovalentGeom(sel=notKnown)

with

try:
  protocol.genExtendedStructure()
except protocol.CovalentViolation:
  pass

best regards--
Charles


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