AMBER Archive (2009)

Subject: Re: [AMBER] QQD psuedoatom restraints

From: David A. Case (
Date: Fri May 29 2009 - 10:18:29 CDT

On Fri, May 29, 2009, Titus, Jamie (bairdje) wrote:

> The line in the map.DG-AMBER file implies to me that the
> restraint between two QQD atoms would be extrapolated to the two CG
> atoms PLUS 2.2 Angstroms.

I agree with your interpretation, but the code actually never uses the 2.2
Ang. distance correction (!?!).

So, you could manually add it to your input files. Or you could apply the
attached patch file to makeDIST_RST.c -- check the outputs carefully to make
sure you are getting what you want.

Thanks for the report. And let me know if the patch (simple, but untested!)
doesn't work correctly.


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