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ddg_monomer conformational search...

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ddg_monomer conformational search...
#1

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?

B) 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?

AttachmentSize
options.txt611 bytes
Post Situation: 
Wed, 2012-05-09 11:10
yperez

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.

Sat, 2012-05-12 07:16
yperez

Did you have ddg_predictions.out and mutant_traj*** files outputed? What does your mut.mutfile look like?

Thu, 2012-05-24 14:22
deltag

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
1
H 55 D
1
G 78 L

The 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.

Mon, 2012-06-11 09:35
yperez

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.

Mon, 2012-10-22 07:11
yperez

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.

Mon, 2012-10-22 07:11
yperez