Hello,
I'm not sure if this is the best solution, but you can try this. Whatever
leaprc you are loading into leap (i.e. ff99SB, or what have you), copy that
file into your local directory like so:
cp $AMBERHOME/dat/leap/cmd/leaprc.ff99SB leaprc
Then edit it, commenting out or deleting the addPdbResMap section that maps
the chain-terminating amino acids and nucleic acids to the N- and C-terminal
amino acids and 5'- and 3'- terminal nucleic acids. Keep in mind that if
you do this, you'll have to manually insert the residue name "NXXX" and
"CXXX" for any N- or C-terminal amino acid you actually do want in your
protein. When you load leap, that file should be automatically loaded, so
you can leave out the "source leaprc.xxxx" command.
Hope this helps,
Jason
On Mon, Sep 27, 2010 at 12:51 AM, Hugh Cheng <pnnler.gmail.com> wrote:
> Dear all,
>
> I have a protein with 4 helices. All the 4 N terminals connect to the
> same organic molecule. No matter how I use "remove" or "bond" commands in
> the leap program, I can always get only one N terminal of a helix which
> attaches the molecule and all the other three keep unattached, because I
> always observe the "N3" atom type instead of "N" for the other 3 N-terminal
> amino acids. Is it any way that the leap program can disable looking for N
> terminals? In my case the organic molecule plays the role of 4 N terminals.
>
> Thanks ahead,
> Hugh
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Sep 27 2010 - 04:30:08 PDT
