Finally i was able to create 10000 models of my 90 residues protein.
By running cluster.linuxgccrelease i got (i guess) 560 clusters:
Additional Clustering: 513s
But now i don't know what to do.
According to the IsThisModelGood.pdf document, now i have to create a plot RMSD vs score, so as i don't have a crystal structure to use as a reference, i think the best idea will be to use the structure with the lowest energy, right?
The problem is that i want to use the score application in order to find it, but then i realised that there are 8 different executables:
score_aln2.linuxgccrelease, score_aln.linuxgccrelease, score_jd2.linuxgccrelease, score.linuxgccrelease,
score_aln2.omp.linuxgccrelease, score_aln.omp.linuxgccrelease, score_jd2.omp.linuxgccrelease and score.omp.linuxgccrelease.
Which one should i used? What is the difference between all of them?
The structure with the lowest energy should belong to the bigger cluster, am i correct? What will happening if this not occur?
I have tons of questions, but i can't find a tutorial out there :/
Hope someone can help me,