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

[Thomas Evangelidis]

This is a bit off-topic but if you want to improve dihedral angles, bond
angles and distances, rotamers along with steric clashes, IMO PyRosetta is
more efficient than GROMACS. I use ClassicRelax protocol with the 'standard'
score function in conjunction with the 'score12' patch ('score12' patch is
not included in the example script) that incorporates terms for ramachandran
and omega angles. The only drawback is that the current version 1.1 does not
allow you to apply distance restraints. This feature will be available in
the new version which will be released sometime in January.

Additional improvements can been done by flipping side-chains to adopt
statistically favourable conformations. SCWRL4 is nice choice and is
recommended for homology models derived from low sequence similarity
templates and BEFORE energy minimization. Great care should also be taken to
preserve side-chain conformation of biologically important residues (i.e. in
the active site of an enzyme). SCWRL4 will probably flip them too, which is
something you wouldn't want. You can correct that by editing the .pdb file
upon processing with SCWRL4. You can also do side chain optimization
manually with the UCSF Chimera GUI.

hope this helps,

Thomas



On 9 December 2010 18:22, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>
>>
>>
>>
>>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101210/dfc76f30/attachment.html>