[gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?

[Justin A. Lemkul]

Arthur Roberts wrote:
> Hi, all,
> 
> I am looking for a way in gromacs or manually to make all the angles, 
> etc. ideal.  Perhaps, there is a way to energy minimize a specific 
> subset of residues or a single residue.  Your advice would be greatly 
> appreciated.
> 

Couldn't you just specify very strong force constants for all the bonds, angles, 
etc?  Even in the absence of increased force constants, an in vacuo minimization 
should produce pretty good geometry, should it not?  Using constraints should 
help as well, even perhaps "constraints = all-angles."

To minimize only a subset, you could perhaps freeze the other atoms, but that 
can be tricky depending on the rest of the .mdp settings.  Perhaps a strong 
position restraint on anything you don't want to move?  You can use genrestr 
with a custom index group to specify the atoms to be restrained.

-Justin

> Sincerely,
> Art
> 
> Dr. Arthur Roberts, Ph.D.
> University of California, San Diego
> Skaggs School of Pharmacy and Pharmaceutical Sciences
> 9500 Gilman Drive #0703
> La Jolla, CA 92093-0703
> email: a1roberts at ucsd.edu <mailto:a1roberts at ucsd.edu>
> cell: 206-850-7468
> office: 858-822-7804
> fax: 858-246-0089
> 
> 
> 
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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