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PostPosted: Thu Apr 05, 2012 8:52 pm 
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After running multiple tests with the protein and ligand that I am trying to dock, I cannot get the pre-compiled and built from source versions of Vina to produce the same result. I have kept everything the same; the same random seed, the same input pdbqt files and the same configuration file. Can anyone tell me why the two versions are not coming from the same source code? Or whether the random seed in the options does not control all of the pseudo-randomness used in the docking calculations?

One more thing, the reason for using the built from source version of Vina was my hope of solving another Vina problem. I know that past questions have come up about the number of modes outputted by Vina. I know that it has been said that this can be controlled using only the num_modes and energy_range options, but I have found this not to be the case. No matter how high I go with those two options, I can get no more than 20 results. However, the source code contains a line limiting the number of saved minimum values at 20. If I change this to num_modes, I can get all the modes I want. However, I do not know what effect this has on the docking calculations. Could anyone help me solve this problem and discrepancies in versions?

Thanks,
Peter


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PostPosted: Thu Apr 05, 2012 10:45 pm 
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PTalpey wrote:
After running multiple tests with the protein and ligand that I am trying to dock, I cannot get the pre-compiled and built from source versions of Vina to produce the same result. I have kept everything the same; the same random seed, the same input pdbqt files and the same configuration file. Can anyone tell me why the two versions are not coming from the same source code? Or whether the random seed in the options does not control all of the pseudo-randomness used in the docking calculations?

One more thing, the reason for using the built from source version of Vina was my hope of solving another Vina problem. I know that past questions have come up about the number of modes outputted by Vina. I know that it has been said that this can be controlled using only the num_modes and energy_range options, but I have found this not to be the case. No matter how high I go with those two options, I can get no more than 20 results.


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However, the source code contains a line limiting the number of saved minimum values at 20. If I change this to num_modes, I can get all the modes I want. However, I do not know what effect this has on the docking calculations. Could anyone help me solve this problem and discrepancies in versions?

Thanks,
Peter


See the FAQ that starts with "I changed something and ...". I think it applies in your case, unless you changed more than you think. Simply using different compilers/libraries can introduce arbitrary differences equivalent to using a different seed.

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PostPosted: Fri Apr 06, 2012 1:52 am 
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... specifically the transcendental functions (sin, cos), can give slightly different results on different machines. The differences can accumulate, etc., so that they behave like choosing a different seed.

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