AMBER Archive (2006)

Subject: Re: AMBER: ambpdb -pqr

From: Carlos Simmerling (
Date: Tue Nov 28 2006 - 15:03:18 CST

page 283 of the manual lists the ambpdb syntax.
-pqr is not a flag for the prmtop, you need -p for that.

Seth Lilavivat wrote:

>Dear Amber Community,
>I am attempting to write a PQR file by using the -pqr flag on ambpdb. However,
>when I offer the command I receive an error:
> ambpdb -pqr myfile.prmtop < myfile.inpcrd > newfile.pqr
>When I open up "newfile.pqr" it says, "Unknown flag myfile.prmtop".
>Thanks for everyone's help,
>The AMBER Mail Reflector
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