I am trying to use relax.linuxgccrelease to remove any clashes in my PDB file.
Can I ask
1) As I understand from "3) Preparing Your Structure.pdf" in the "introduction" tutorial from Meiler Lab, I should use
relax.linuxgccrelease -database <database> -s <structure> -ex1 -ex2 -relax:sequence -nstruct 100
However, I have been told that:
ERROR: Unused "free" argument specified: -database
So I delete the "-database" option, and run the following, which seems to be fine.
relax.linuxgccrelease -s <structure> -ex1 -ex2 -relax:sequence -nstruct 100
So "-database" is not necessary?
2) I am trying to understand the syntax by using
However, I still could not get useful information from the help file. I think "-nstruct" is the number of models to be constructed. But what is the meaning of "-ex1", "-ex2" and "-relax:sequence"?
More importantly, why do the flags of "-ex1", "-ex2" and "-relax:sequence" not exist in the help file? How actually can I learn to use flags/options from help files?
3) Can I ask is there an on-line database for all the syntax of the executables? Therefore, I do not necessarily need to type "-help" for help.
Thank you very much.