Hi,<br><br>We've been working with ProtPred-PEO-Gromacs project [1]. In general lines, this project is a implementation of NSGA-II algorithm in Gromacs to discover a minima energy of protein conformation . NSGA-II is a Multi-Objective Evolutionary Algorithm (MOEA).<br>
<br>More specific in Gromacs implementation, this project is a multi-system as REMD simulation. However, the new protein conformations are obtained from genetic operators. In [2] there is a simple documentation wrote by me to publish the some project ideas about it.<br>
<br>The integrator option is peo instead of md and its function is do_peo in md.c. This project is under development version. My genetic operators work with the protein backbone angles. This representation is common for MOEAs when is working with proteins.<br>
<br>In this way, I've studied about g_dhi program. I found the dih_angle function in bondfree.c. This function computes all backbone angles storing them in t_xrama structure represented by xr variable. <br>
<br>Because of my simulation is a multi-system, I have for each system (protein conformation) a trr file. I need ideas to help me to obtain my backbone angles without call g_dhi routines.. <br><br>I thought to compute the backbone angles in my integration function (do_peo) because it has all atoms. So, I want to
call a function which computes the backbone angle of my protein such as:
<br>t_peo_phipsi compute_backbone(t_mdatoms *mdatoms). <br><br>Any comments for a good way to do this? Or other ways?<br><br>[1] <a href="http://gitorious.org/protpred-peo/gromacs" target="_blank">http://gitorious.org/protpred-peo/gromacs</a><br>
[2] <a href="https://docs.google.com/fileview?id=0ByNUaKmUm2WoNDRlZDkwYmYtNTBhMS00NGUwLWI1MDMtOWEzMjNmY2I4OGQ5&hl=en" target="_blank">https://docs.google.com/fileview?id=0ByNUaKmUm2WoNDRlZDkwYmYtNTBhMS00NGUwLWI1MDMtOWEzMjNmY2I4OGQ5&hl=en</a><br>
<br><br>Thanks in advance,<br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>
University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a><br>
Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a><br>Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>