Hello Changdong--
>
> 1)
> dock_pre.py(84): rampedParams.append( MultRamp(0.05,1.0, "pre.setScale(
> VALUE )") )
> dock_pre.py(88): from residueAffPotTools import create_ResidueAffPot
> dock_pre.py(89): ra = create_ResidueAffPot('hydphob',
> interdomainContacts=True,
> dock_pre.py(90): potentialName="Miyazawa")
> create_residueAffPot: residue GUA not known
> create_residueAffPot: residue CYT not known
> .....
>
> I've checked the manual the "Miyazawa" is used for protein, just
> disregarded the messages,right?
Correct. There are currently no terms for nucleic acids.
>
> 2)In the .viols files, the difference between obs and cal PRE values is
> very large for the PRE restraints. Are there any parameters in prePot I
> need to adjust?
First make certain that your correlation time and other PRE parameters
(e.g. eSpinQuantumNumber and frequency) are reasonable, particularly
if there are systematic differences. After that, you can try
increasing the PRE force constant (called scale in the script).
best regards--
Charles
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