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AMBER Archive (2009)Subject: RE: [AMBER] QQD psuedoatom restraints
From: Titus, Jamie (bairdje) (BAIRDJE_at_UCMAIL.UC.EDU)
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!
On Fri, May 29, 2009, Titus, Jamie (bairdje) wrote:
> The line in the map.DG-AMBER file implies to me that the
I agree with your interpretation, but the code actually never uses the 2.2
So, you could manually add it to your input files. Or you could apply the
Thanks for the report. And let me know if the patch (simple, but untested!)
...thanks...dac
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