<br>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.<br>
<br>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.<br><br>hope this helps,<br><br>Thomas<br><br><br><br><div class="gmail_quote">
On 9 December 2010 18:22, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
Arthur Roberts wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi, all,<br>
<br>
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.<br>
<br>
</blockquote>
<br></div>
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."<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
Sincerely,<br>
Art<br>
<br>
Dr. Arthur Roberts, Ph.D.<br>
University of California, San Diego<br>
Skaggs School of Pharmacy and Pharmaceutical Sciences<br>
9500 Gilman Drive #0703<br>
La Jolla, CA 92093-0703<br></div>
email: <a href="mailto:a1roberts@ucsd.edu" target="_blank">a1roberts@ucsd.edu</a> <mailto:<a href="mailto:a1roberts@ucsd.edu" target="_blank">a1roberts@ucsd.edu</a>><div class="im"><br>
cell: 206-850-7468<br>
office: 858-822-7804<br>
fax: 858-246-0089<br>
<br>
<br>
<br>
<br>
<br>
<br>
</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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