AMBER Archive (2008)

Subject: Re: AMBER: LEaP problem with LEU first residue?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Oct 14 2008 - 05:41:01 CDT

have you tried using the prmtop/inpcrd and ambpdb to make the pdb?
perhaps leap is putting the H numbers in the previous column, which is
correct for some H and not others (I never can remembers all of the H
column rules).

On Tue, Oct 14, 2008 at 6:26 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> 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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