AMBER Archive (2006)

Subject: Re: AMBER: adding polar hydrogens

From: David A. Case (case_at_scripps.edu)
Date: Wed Oct 11 2006 - 11:14:29 CDT

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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