Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file

From: Jason Swails <>
Date: Sun, 27 Jan 2013 09:16:14 -0500

On Sun, Jan 27, 2013 at 3:42 AM, Jonathan Saboury <> wrote:

> Hello, all I want to do is use this .pdb:
> to make a ".prmtop" and ".inpcrd" file so I can input it into OpenMM.
> I am an Intermediate C++ programmer but only know hwo to use windows. I am
> using
> the cygwin installation guide ""

> Here is the error I am getting.
> Any idea what went wrong? I didn't update bc when I do I get this:

This is an easy error to fix -- you need to install the "patchutils" and
"patch" Cygwin packages to provide the 'patch' command. A more
comprehensive list of packages that you need to install can be found here:

Make sure you install those packages listed, then try again.

If it still doesn't work, it would help to know what version of Windows you
are trying to use. I've worked successfully on Windows XP and heard
similar success stories on Windows 7, but I can't speak for other versions.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Sun Jan 27 2013 - 06:30:02 PST
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