Hello,
Per our previous discussion on QQD psuedoatom restraints, I would also like to make sure an unusual arginine restraint would work properly as well.
If I modify the map.DG-AMBER file with the following line:
QQHH = CZ 2.1
which was calculated by computing the distance between the CZ atom of arginine to each of the atoms 1HH1, 1HH2, 2HH1, and 2HH2, taking the longest distance of the four, and adding a twentieth of an angstrom.
Will this restraint work properly during sander, and is this the proper way to include a restraint to this degenerate chemical shift?
Thanks!
Jamie
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of David A. Case [case.biomaps.rutgers.edu]
Sent: Friday, May 29, 2009 11:18 AM
To: AMBER Mailing List
Subject: Re: [AMBER] QQD psuedoatom restraints
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.
...thanks...dac
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Received on Mon Jul 06 2009 - 08:53:07 PDT
