I'm trying to add polar hydrogens to a PDB file using PROTONATE.exe (oringinally from autodock, I think). I tried the command lines with the executable, but could not generate the desired output PDB file. If anyone knows the proper command line calls (perhaps an example), please advise.
I tried the following:
protonate.exe < name.pdb > out.pdb
which generated:
PROTON_INFO, protonate.exe.stackdump, and out.pdb
The only file with anything in it was the stackdump
Stack trace:
Frame Function Args
End of stack trace
Do I need to use PROTON_INFO.kollua_polH, as in:
protonate.exe -k PROTON_INFO.kollua_polH < name.pdb > out.pdb
Because I tried that, also with the "-d" flag an that didn't work either.
Help greatly appreciated.
Sean
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Received on Wed Oct 11 2006 - 06:07:25 PDT
