On Thu, Apr 07, 2005, Kara Di Giorgio wrote:
> I'm trying to set distance restraints between some protein sidechains
> and a structural calcium ion. The calcium leaves its pocket and the
> protein begins to unravel without any constraints. I made a upb file
> and tried to use make DIST_RST and got the following error message:
>
> makeDIST_RST -upb carestraints.upb -pdb enzph1ala_min3.pdb -rst
> enzph1ala_rst_min3.rst
> # makeDIST_RST
> Currently configured for up to 5000 atoms
> Using MAP file /usr/local/amber/dat/map.DG-AMBER
> ERROR no map function for CA CA :data= 79 GLY O 171 CA CA 2.8
Same suggestion as in my last e-mail: use the "raw" sander format, described
in section 5.9. makeDIST_RST is primarily a time-saving front end that is
useful for handling lots of "ordinary" NMR constraints. When you need to
handle things that makeDIST_RST doesn't understand, you should do it by hand.
Of course, your final sander input file can include some constraints created
by makeDIST_RST, and others that you wrote yourself.
....good luck...dac
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Received on Fri Apr 08 2005 - 16:53:01 PDT
