AMBER Archive (2006)

Subject: AMBER: adding polar hydrogens

From: Sean Rathlef (
Date: Tue Oct 10 2006 - 21:43:39 CDT

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.

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