weights for pH_protocol

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    • April 26, 2017 at 2:14 pm #2646
      Anonymous

        Dear all,

        I have been recently testing pH_protocol to calculate the pKa of one of my proteins. In the original paper, the authors include the weights function to be used with the protocol:

        fa_atr 0.8

        fa_rep 0.44

        fa_sol 0.65

        fa_intra_rep 0.004

        fa_dun 0.56

        hbond_lr_bb 1.17

        hbond_sr_bb 1.17

        hbond_bb_sc 1.17

        hbond_sc 1.1

        hack_elec 1.0

        e_pH 1.0

        ref 1.0 

         

        After replacing hack_elec to fa_elec everything works fine. However, while the results are mostly the same as the ones I get from running on ROSIE, a couple of sidechains get really different Pkas. Any ideas?

        Regards

        Felipe

      • April 27, 2017 at 2:10 pm #12313
        Anonymous

          Here’s the weights that the ROSIE server is using for the pKa protocol: 


          
fa_atr 0.8
          
fa_rep 0.44
          
fa_sol 0.75
          
fa_intra_rep 0.004
          
fa_elec 1.0
          
e_pH 1.0
          
pro_close 1
          
hbond_sr_bb 1.17
          
hbond_lr_bb 1.17
          
hbond_bb_sc 1.17
          
hbond_sc 1.1
          
dslf_fa13 1.0
          
rama 0.2
          
omega 0.5
          
fa_dun 0.56
          
p_aa_pp 0.32
          
ref 1

          And here’s the equivalent command that’s being run: 


          
pH_protocol.linuxgccrelease -s protein.pdb -ignore_unrecognized_res -ignore_waters -pH_mode -pka_all -ex1 -ex1:level 3 -ex2 -ex2:level 3 -extrachi_cutoff 0 -use_input_sc -score:weights custom.wts -no_output -pH_neighbor_pack -pka_rad 6.0 -pH_prepack

          Hopefully that will help you get started to debug the difference.

          Also, keep in mind that Rosetta runs are typically stochastic. Multiple runs will result in slightly different values. How different depends on the system and the protocol. If the variation is small, it might just be a difference in run-to-run variability. I might suggest running the local runs several times to get a sense of the size of the stochastic variation.

        • April 27, 2017 at 2:10 pm #12834
          Anonymous

            Here’s the weights that the ROSIE server is using for the pKa protocol: 


            
fa_atr 0.8
            
fa_rep 0.44
            
fa_sol 0.75
            
fa_intra_rep 0.004
            
fa_elec 1.0
            
e_pH 1.0
            
pro_close 1
            
hbond_sr_bb 1.17
            
hbond_lr_bb 1.17
            
hbond_bb_sc 1.17
            
hbond_sc 1.1
            
dslf_fa13 1.0
            
rama 0.2
            
omega 0.5
            
fa_dun 0.56
            
p_aa_pp 0.32
            
ref 1

            And here’s the equivalent command that’s being run: 


            
pH_protocol.linuxgccrelease -s protein.pdb -ignore_unrecognized_res -ignore_waters -pH_mode -pka_all -ex1 -ex1:level 3 -ex2 -ex2:level 3 -extrachi_cutoff 0 -use_input_sc -score:weights custom.wts -no_output -pH_neighbor_pack -pka_rad 6.0 -pH_prepack

            Hopefully that will help you get started to debug the difference.

            Also, keep in mind that Rosetta runs are typically stochastic. Multiple runs will result in slightly different values. How different depends on the system and the protocol. If the variation is small, it might just be a difference in run-to-run variability. I might suggest running the local runs several times to get a sense of the size of the stochastic variation.

          • April 27, 2017 at 2:10 pm #13355
            Anonymous

              Here’s the weights that the ROSIE server is using for the pKa protocol: 


              
fa_atr 0.8
              
fa_rep 0.44
              
fa_sol 0.75
              
fa_intra_rep 0.004
              
fa_elec 1.0
              
e_pH 1.0
              
pro_close 1
              
hbond_sr_bb 1.17
              
hbond_lr_bb 1.17
              
hbond_bb_sc 1.17
              
hbond_sc 1.1
              
dslf_fa13 1.0
              
rama 0.2
              
omega 0.5
              
fa_dun 0.56
              
p_aa_pp 0.32
              
ref 1

              And here’s the equivalent command that’s being run: 


              
pH_protocol.linuxgccrelease -s protein.pdb -ignore_unrecognized_res -ignore_waters -pH_mode -pka_all -ex1 -ex1:level 3 -ex2 -ex2:level 3 -extrachi_cutoff 0 -use_input_sc -score:weights custom.wts -no_output -pH_neighbor_pack -pka_rad 6.0 -pH_prepack

              Hopefully that will help you get started to debug the difference.

              Also, keep in mind that Rosetta runs are typically stochastic. Multiple runs will result in slightly different values. How different depends on the system and the protocol. If the variation is small, it might just be a difference in run-to-run variability. I might suggest running the local runs several times to get a sense of the size of the stochastic variation.

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