sam

sdsort, sdreport and sdfilter problem

improving the accuracy- optimizing the docking parameters

Hi Sergi, I am using rdock for docking RNA-ligand, but with my HTVS ligand file, I am getting a Segmentation fault (I have splitted my files so split1.sd is one of them). I am not sure what is wrong with my input files and I would appreciate I you help me with it. I also used the DUD (ace) test files for my ligand database but still I am getting the same error. I appreciate it if you help me with this. I am using these command : rbcavity -r rdock.prm -d -was > cavity.log rbdock -r rdock.prm -p dock.prm...

Hi sergio, Thank you very much for your reply. You actually pointed out thr prolem. By visualizing I noticed my ligand is not defined in the vicinity of the receptor. How should I put the ligand in the vicinity of receptor? or what software or method I should use to define that? rbcavity -was -d -r <prmfile> will only creat a box around the ligand. Please help me with that so I can proceed with my simulation. </prmfile> Thanks a lot in advance. Bests, Sam

Hi Sergi, Thank you for your reply. I defined the cavity. I have attached the outputs of running these commands: rbcavity -r rdock.prm -was > rna_cavity.log rbdock -r rdock.prm -p dock.prm -n 100 -i ligand.sd -o rna_docking_out > rna_docking_out.log sdsort -n -f'SCORE' rna_docking_out.sd > 2qwy_docking_out_sorted.sd sdrmsd ligand.sd 2qwy_docking_out_sorted.sd But still getting the same results. I can tell after running rbcavity commands the caviy has been determinded in the log file. Please let me...

I was wondering if anybody can hep me with this problem??

no interaction with ligand and mol2