Question: Trouble Interpreting Warning Messages When Performing Homology Modeling With Gromacs And Procheck
0
gravatar for Elmo
7.6 years ago by
Elmo130
Elmo130 wrote:

Hi experts,

Need advice! I performed homology modeling using HHpred with two approaches:

1) Local alignment. I selected all 20 templates generated. [Note: all the templates only cover the query sequence from residue 150 onwards though].

2) All options are as default, except using global alignment [to obtain templates in fragments for residue 1 - 150, and the rest of the query sequence, in total of 20 templates].

I then performed energy minimization using Gromacs. And then Procheck for validation. For the first approach, there are some error such as:

  • Ramachandran plot: 90.1% core 7.0% allow 1.8% gener 1.0% disall
  • All Ramachandrans: 18 labelled residues (out of 571)
  • Residue properties: Max.deviation: 4.4 Bad contacts: 18 * Bond len/angle: 8.5 Morris et al class: 1 1 2 G-factors Dihedrals: -0.02 Covalent: -0.33 Overall: -0.13
  • M/c bond angles: 91.8% within limits 8.2% highlighted 1 off graph

For the second approach, there was a warning:

  • Warning: fopen(/var/www/html/Services/SAVES3/jobs/483990/procheck/protein.sum) [function.fopen]: failed to open stream: No such file or directory in /var/www/html/Services/SAVES3/utils.php on line 145 Cannot PROCHECK find or open: /var/www/html/Services/SAVES_3/jobs/483990/procheck/protein.sum

My question is, can I still proceed with further analysis such as protein docking to study its binding site and all for the protein generated in the first approach (with the error and all, plus, the residues from 1 - 150 were constructed without homology). And why is there a warning for the validation for the second approach when I randomly select the templates for the global alignment mode?

Please advice. Thanking you all in advance! :)

• 2.1k views
ADD COMMENTlink modified 7.6 years ago by Aloctavodia30 • written 7.6 years ago by Elmo130
0
gravatar for Aloctavodia
7.6 years ago by
Aloctavodia30
Aloctavodia30 wrote:

It sound like a problem on the server (and not necessarily with your data) I guess you run procheck from here http://nihserver.mbi.ucla.edu/SAVES/ In that case you should write to holton at mbi. ucla. edu explaining your problem.

ADD COMMENTlink written 7.6 years ago by Aloctavodia30
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