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Re: [modeller_usage] Restrain Uses in MODELLER v.91.6



On 10/3/16 1:47 AM, Sushil Mishra wrote:
I am trying to model a protein with certain distance restraints and
disulphide bonds. I wonder why restraint does not work when I set
disulphide bonds.

What do you mean by "does not work"? Your script looks fine to me.

What can be the
reason that it does not work with S-S restraints. Moreover, Is there a
way to control force constant for harmonic restraints in such cases ?

Technically, you are not adding an S-S restraint - you are telling Modeller that the two disulfides are bonded, so when it turns on the CHARMM forcefield you'll get a term in the scoring function that corresponds to the S-S bond. So if you want to adjust that force constant (I can't imagine why you'd want to) the way to do it would be to edit the CHARMM parameter file, modlib/par.lib (in the BOND section, which is arranged by CHARMM atom type; the two S atoms are type SM, so you'd be looking around line 291 in Modeller 9.17).

	Ben Webb, Modeller Caretaker
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             https://salilab.org/modeller/
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