On Tue, Oct 10, 2006, Sean Rathlef wrote:
>
> 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
Some more information would help a lot:
1. What is in "out.pdb"?
2. Which version of Amber? (I'm assuming this is cygwin(?); which compiler?)
3. Do you have the $AMBERHOME environment variable set correctly?
4. Is the PROTON_INFO file empty? (That would suggest that $AMBERHOME
is not set correctly.)
>
> Do I need to use PROTON_INFO.kollua_polH, as in:
> protonate.exe -k PROTON_INFO.kollua_polH < name.pdb > out.pdb
If you want to use this file, which I assume you made yourself, then you
certainly need to specify it with the "-d" flag.
I doubt that your problem has anything to do with command-line flags.
...dac
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Received on Thu Oct 12 2006 - 20:36:06 PDT
