AMBER Archive (2008)

Subject: AMBER: LEaP problem with LEU first residue?

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 14 2008 - 05:26:25 CDT

I posted yesterday about alleged problems of add-H with leap. However,
the message included follow up with Amber components in DOCK. Probably
the (reasonable) reason why I had no answer.

Now I am restricting my problem to Amber10 and AmberTools1.2. I have
repeated generation of full-atoms file with leap and ambpdb,
confirming previous outcome.

Starting noh file:

TOM 1 N LEU A 1
ATOM 2 CA LEU A 1
ATOM 3 CB LEU A 1
ATOM 4 CG LEU A 1
ATOM 5 CD1 LEU A 1
ATOM 6 CD2 LEU A 1
ATOM 7 C LEU A 1
ATOM 8 O LEU A 1

Resulting pdb, created from prmtop/inpcrd:

ATOM 1 N LEU 1
ATOM 2 1H LEU 1
ATOM 3 2H LEU 1
ATOM 4 2H LEU 1
ATOM 5 CA LEU 1
ATOM 6 HA LEU 1
ATOM 7 CB LEU 1
ATOM 8 2HB LEU 1
ATOM 9 3HB LEU 1
ATOM 10 CG LEU 1
ATOM 11 HG LEU 1
ATOM 12 CD1 LEU 1
ATOM 13 1HD1 LEU 1
ATOM 14 2HD1 LEU 1
ATOM 15 3HD1 LEU 1
ATOM 16 CD2 LEU 1
ATOM 17 1HD2 LEU 1
ATOM 18 2HD2 LEU 1
ATOM 19 3HD2 LEU 1

What I am asking here is if hydrogens have been added correctly to LEU
as first residue, focusing the attention to hydrogen names for atoms
2-4. From Amber, I would have expected

2 H1
3 H2
4 H3

however, I have no previous experience with LEU as first residue in
Amber. I wonder whether the error is with these atom names. If not,
the module in DOCK is unable to treat correctly leap-protonated LEU as
first residue. In that case I'll ask to dock users.

Must add that I am using AmberTools 1.2 for the first time. So far,
with Amber 10 I had AmberTools 1.0.

Thanks
francesco pietra
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