Subject: Re: [modeller_usage] ERROR IN MODELS ASSESSMENT
From: Modeller Caretaker <>
Date: Mon, 12 Dec 2016 10:30:00 -0800
On 12/12/16 5:10 AM, Mahesh Velusamy wrote:
This is to inform you that I have introduced new residue type called BGC
which has a Glycosidic linkage between ASP and Beta-D-GLUCOSE as mentioned
in the following protocol https://salilab.org/modeller/6v2/FAQ.html#2. I
can access this newly introduced residue successfully throughout the
modeling but after the models generation I get the following warning
message for the single models assessment.
Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: BGC:N BGC
DOPE is a statistical potential, so it's trained on known protein
structures. Obviously we didn't include any of your BGC residues in the
training set, so you should expect to see such a warning.
preppdf_453W> No fixed restraints selected; there may be some dynamic ones.
preppdf_454W> Restraints file was probably not read; use restraints.append().
Here, I just want to know what does these statements implies "No fixed
restraints selected; there may be some dynamic ones. Restraints file was
probably not read; use restraints.append()"
These look fine too. Usually when you evaluate the scoring function you
have at least some static restraints, such as stereochemistry, so
Modeller will warn you if you try to evaluate the score without any
static restraints. But DOPE consists entirely of dynamic restraints, so
no problem here.