AMBER Archive (2004)

Subject: AMBER: One more question about the tree structure of looping residues

From: Yuhui Cheng (amberuser3_at_yahoo.com)
Date: Wed Aug 25 2004 - 22:11:36 CDT

Hi,
   I noticed one more problem about the amino acids
having loops(such HIS, PHE, TYR & TRP). If you use the
leap to generate the topology file, and then check the
tree structures of residues which have loops, you'll
find that it's different from the order in
$AMBERHOME/dat/leap/prep/all_amino94.in
   For example as HID and HIE:
   The tree structures in the original prep library:
   HID: MEME3EE(SBEBESSE)ME
   HIE: MEME3EE(SSBEBESE)ME
   In my protein:
   HID: MEME3EE(BSESESBE)ME
   HIE: MEME3EE(BESEBEBE)ME
   However, if you check the atom name or atom type
matrix, the order is exactly the same with the
original prep library. Therefore, the tree labels for
some atoms in the loops are changed. Does it necessary
to change? Why does it happen? I checked TRP,TYR, and
PHE as well, similar changes were noticed.

Thanks,
Yuhui

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