AMBER Archive (2009)

Subject: RE: [AMBER] QQD psuedoatom restraints

From: Titus, Jamie (bairdje) (BAIRDJE_at_UCMAIL.UC.EDU)
Date: Fri May 29 2009 - 14:01:34 CDT


I applied the patch to /usr/local/amber10/src/nmr_aux/prepare_input/makeDIST_RST.c using the following:
patch -p0 -N < dist.patch
make -f Makefile_at

which both completed without error.

I examined makeDIST_RST.c to ensure that the proper lines were added or deleted - they were.

I reran makeDST_RST on my input file.

restraint in CYANA format:
13 LEU QQD 16 LEU QQD 3.61 #peak 191

restraint in output RST file:
# 13 LEU QQD 16 LEU QQD 3.61 (#peak 191)
  ixpk= 191, nxpk= 0, iat= 226, 277, r1= 1.30, r2= 1.80, r3= 3.61, r4= 4.11, &end

which is the same as before the patch, and when I use sander to apply the restraints and analyze the POUT file, I see the following:

 CG LEU 13 -- CG LEU 16: 4.936 3.610 1.326 21.524 d 191: 0

Which implies that nothing has changed. When should the switch from QQD nomenclature switch to CG nomenclature (in the output of makeDIST_RST)? Obviously, the mapping of QQD to CG is occurring during the sander run, but the 2.2 angstroms is not being added. Why would the switch from QQD to CG not occur in the output of makeDIST_RST. Is that where it should be occurring?

Thanks for the help.

From: [] On Behalf Of David A. Case []
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.


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