I need some help for using pHDock applications(histidine protonation / pH-dependent binding)

[Anonymous]

Hi everyone

I’m beginner of ROSETTA/Linux commandline, so please explain problems easily

I can model protonated histidine residue(HIS_P?) by docking_prepack application

mkdir pre_pHDock_5.0



docking_prepack_protocol.static.linuxgccrelease  

-s Y29Hbr/3qwq_D1_prep_0001_Y29H_br_0001.pdb 

-dock_ppk 

-pH:pH_mode -pH:value_pH 5.0 

-ex1 -ex2aro 

-score:weights pH_standard.wts 

-out:path:all ./pre_pHDock_5.0

But when I execute docking_protocol application, my protonated histidine(HIS_P) goes back to normal histidine(HIS)

mkdir pHDock_5.0_fix



docking_protocol.static.linuxgccrelease  

-s pre_pHDock_5.0/3qwq_D1_prep_0001_Y29H_br_0001_0001.pdb 

-partners A_B 

-pH:pH_mode -value_pH 5.0 

-keep_input_protonation_state 

-docking_local_refine 

-ex1 -ex2aro 

-nstruct 50 

-out:path:all ./pHDock_5.0_fix

what is my problems and how can I solve them

[Anonymous]

Umm… 

I can model protonated histidine docikng via score option (from pKa)

I will test other proteins and update this post

docking_protocol.static.linuxgccrelease  

-s Y29Hbr/3qwq_D1_prep_0001_Y29H_br_0001.pdb 

-partners A_B 

-pH:pH_mode -value_pH 5.0 

-docking_local_refine 

-ex1 -ex2aro 

-nstruct 10 

-score:weights pH_standard.wts 

-out:path:all ./pHDock_5.0_np

 

[Author]

Posts