Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › ddg_monomer conformational search…
- This topic has 5 replies, 2 voices, and was last updated 11 years, 11 months ago by Anonymous.
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May 9, 2012 at 6:10 pm #1274Anonymous
Hi,
I’m fairly new to using Rosetta suite, so sorry if silly questions. I’m running ddg_monomer app for a protein of about 150 aa.A) the pdb outputs I get are all the same, there is no backbone or sidechain movement neither for wt nor for mut structures (50 for each as recommended). I intended to carry out the protocol of row 16 in Kellogg, 2011. I attached the options file, if you’d be so kind to take a look at it. What am I missing here?
I’m working in a 2GB RAM PC. After a while, I got the process Killed (just that in shell prompt), and I guess it was due to memory overload, I checked memory consumption. The process starts over 45% memory usage and ramps to 65% in a half hour when the process stops without completion. Can anyone tell me what I’m doing wrong, or I just need a better PC?
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May 12, 2012 at 2:16 pm #7106Anonymous
I have already run the app in a 4Gb RAM PC and it worked, but still no conformational search is done, the 50 structures remain the same. I have tried changing different options without success.
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May 24, 2012 at 9:22 pm #7148Anonymous
Did you have ddg_predictions.out and mutant_traj*** files outputed? What does your mut.mutfile look like?
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June 11, 2012 at 4:35 pm #7227Anonymous
Hi deltag,
Thanks for your reply, sorry to read it so late. The answer is YES, I have those outputs (noted that the mut_traj file is empty). Thats the reason it took me some time to come back, I trusted the ddg_predictions output and moved on, but I am still troubled with the fact that there is so litle deviation among the output structures, my concern is that the conformational search is not properly done in the way I setted the program. I used the long version of the mutfile:total 2
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H 55 D
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G 78 LThe output mutant structures are identical to the wt, except in the mutated residue. Neighboring residues are not disturbed in any way, wich is very unusual.
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October 22, 2012 at 2:11 pm #7968Anonymous
I found that when using -ddg:dump_pdbs false (which does not write pdb outputs) memory consumption is far lower, perhaps because the structure information is stored transiently (in RAM) when calculating. Hope this can help someone.
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October 22, 2012 at 2:11 pm #7969Anonymous
I found that when using -ddg:dump_pdbs false (which does not write pdb outputs) memory consumption is far lower, perhaps because the structure information is stored transiently (in RAM) when calculating. Hope this can help someone.
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