AMBER Archive (2009)
Subject: RE: [AMBER] QQD psuedoatom restraints
From: Titus, Jamie (bairdje) (BAIRDJE_at_UCMAIL.UC.EDU)
I applied the patch to /usr/local/amber10/src/nmr_aux/prepare_input/makeDIST_RST.c using the following:
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:
restraint in output RST file:
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.
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!)