Zhanglab forum

Greetings,

I downloaded the 3DRobot package to generate decoys with the number of output decoys = 1000 and RMSD cutoff = 20, and the generation of the decoys worked. However, when I checked the output file, I found only 433 decoys with RMSD <=8.

I am wondering why the number of output decoys and their RMSD is less than what I specified in the parameters (Parameters: decoys = 1000 and RMSD cutoff = 20, and what I got 433 decoys with RMSD <=8 )! and how to generate thousands of decoys with RMSD cutoff = 20!

Your help would be much appreciated!

Thanks & Regards,
Maytha

Dear user,

I am slightly confused. If you want 1000 decoys with RMSD<8A, then why not set the threshold as 8A?

Best
IT Team

Hello,

I apologize for the confusion! My main goal is to generate thousands of decoys with RMSD <=20. I run the 3DRobot package with the parameter: decoys = 1000 and RMSD cutoff = 20 but the number of output decoys that I got is only 433 and their RMSD is <=8A.

The main question is why the number of output decoys and their RMSD is less than what I specified in the parameters (Parameters: decoys = 1000 and RMSD cutoff = 20, and what I got after running the 3DRobot package is 433 decoys with RMSD <=8 )! and how to generate thousands of decoys with RMSD cutoff = 20!

Thanks for your time!

Dear user,

I got your points, since you only get 443 decoys while you want to 1000, so I guess your program may not be correctly completed, could you check if the default hour 48 is enough for your case? you can set -hour 240 hours to see if things changed.

you can see 8A is 2/5 range of 20A, 443 is roughly 2/5 of 1000 decoys, I assume your programs stoped at 2/5, so try to extend the default time setting.

Best
IT Team