[gmx-users] setting constraints to incomplete protein structures

vivek sharma viveksharma.iitb at gmail.com
Tue Oct 7 08:06:57 CEST 2008

Hi yeo,
I have one query related to the MD you are trying.
 What I understood here is you are trying different conformation of your
protein molecule for docking it with ligand (please, correct me if I am
I am also trying the same, But not finding any criteria to pick up the
conformation of protein to try it further for docking ?
Do you have any insight into the same ?

With Thanks,

2008/10/7 Justin A. Lemkul <jalemkul at vt.edu>

> wk yeo wrote:
>> Hello,
>> My responses are as follows:
>>  My questions:
>>>> 1) Is it a good idea to use such catalytic domain structures for MD
>>>> simulation? Or should I only use complete protein structures for MD?
>>> That depends entirely upon what you are interested in simulating.
>> I am interested in predicting the binding energy (via further processing
>> using a docking software) of a ligand to a specific protein target based on
>> the conformation of the binding pocket after MD.  How will missing residues
>> in the other parts of the protein target affect the MD run for such
>> purposes?
> In biology, structure leads to function.  Missing residues may lead to
> spurious behavior, such as destabilization of the protein structure.
>  2) If I want to use Gromacs to conduct a MD of 0.1ps at 300K, do I need to
>>>> constraint any atoms at the 'edges' during the MD run?
>>> What kind of "edges?" Those that are adjacent to the missing segments? If
>>> that's what you mean, see distance *restraints* or position *restraints*.
>> Yes, I meant atoms that are adjacent to the missing segments. When should
>> I use distance restraints and when should I use position restraints?
> Distance restraints are what you are probably looking for.  You can fix the
> distance between the backbone atoms to the distance found in the crystal
> structure.  As for whether or not you can be confident in doing so is up to
> you.
> Position restraints are typically applied during solvent equilibration to
> allow the solvent to orient around the solute.
>  I have a new question: What if the protein-ligand complex structure
>> obtained from PDB contains chloride ions? How should I handle any ions
>> during the MD runs? Restraint them as well? Or should I just let them go
>> through MD without any restraints?
> If the ions were part of the precipitant or some sort of stabilizing
> co-solvent, they may be unnatural and therefore safe to ignore.  Adding (at
> least) counterions to an MD simulation is routine, so you may end up adding
> those ions back within during solvation.
> -Justin
>  regards,
>> wk yeo
>> _________________________________________________________________
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> --
> ========================================
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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