Subject: Re: [modeller_usage] Single Mutant Script
From: Modeller Caretaker <>
Date: Wed, 3 Apr 2019 17:47:03 -0700
On 4/3/19 5:22 PM, Alex Lian wrote:
I have a few questions about the mutant_model script. I am trying to do
a single mutation modeling using this script.
optimize(s, sched)
s.energy()
Where S represents a group of selected atoms (Mutation position). If I
understand correctly, The optimize function will do a conjugate gradient
to the selected atoms to find the local energy minimum. However, after
doing the minimization step, the energy function results in a small
positive value which is unusual. I also tried selecting the whole
structure which is about 300 residues, did the optimized step and energy
computing. This time the energy function showed up with an extremely
large positive value. Besides this, I tried to compute the DOPE for both
nature structure and the whole sidechain refined structure and found
that the DOPE for the refined model is even larger than the one for the
native structure which made me so confused.
You didn't ask any questions, but this behavior sounds normal to me. The
mutate model protocol is designed to work with everything but the
mutated residue held fixed, so I would not expect it to work
particularly well on the entire model.