AMBER Archive (2008)

Subject: AMBER: Does LEaP understant capping with ACE/NME?

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 21 2008 - 10:57:12 CDT

Hi:

For reasons that would be long to detail, I would like to work
(Amber10) with a model where the first and last residues are capped
with ACE and NME respectively. That for more than one stretch of
standard amino acids. The stretches are separated from one another by
a TER line

The way I have built the pdb file is not undestood by leap.

As an example with one stretch, the first amino acid:

ATOM 1 N LEU 1 xyz
ATOM 2 CA LEU 1
ATOM 3 CB LEU 1
ATOM 4 CG LEU 1
ATOM 5 CD1 LEU 1
ATOM 6 CD2 LEU 1
ATOM 7 C LEU 1
ATOM 8 O LEU 1
ATOM 9 HA LEU 1
ATOM 10 HB2 LEU 1
ATOM 11 HB3 LEU 1
ATOM 12 HG LEU 1
ATOM 13 HD11 LEU 1
ATOM 14 HD12 LEU 1
ATOM 15 HD13 LEU 1
ATOM 16 HD21 LEU 1
ATOM 17 HD22 LEU 1
ATOM 18 HD23 LEU 1
ATOM 19 H LEU 1

The corresponding ACE:

HETATM 4018 C ACE 46 xyz
HETATM 4019 O ACE 46
HETATM 4020 CH3 ACE 46
HETATM 4021 HH31 ACE 46
HETATM 4022 HH32 ACE 46
HETATM 4023 HH33 ACE 46

The various capping residues are NOT separated from one another by a TER line.

LEaP does not understand that there is capping (while Chimera
understands that and reproduces perfectly the whole structure). LEaP
adds a new atom, named H, to each beginning terminal, and "missing"
OXT to each terminal last. Then it tries to join first ACE with last
NME. Perhaps I could avoid the last issue by placing a TER line
between the capping residues but before embarking in a perhaps
hopeless avenue, I ask for experience, or insight.

Without capping, the model is treated correctly by LEaP, though it has
charges that the true protein has not, which does not fit my plans.

Thanks
francesco pietra
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