AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 14 2008 - 08:42:55 CDT

On Tue, Oct 14, 2008 at 12:41 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> have you tried using the prmtop/inpcrd and ambpdb to make the pdb?

This just what I did, as I used to do (successfully) in all previous
cases (never had LEU as first residue, however).
With ff99SB and gaff as ff:

model = loadpdb nohpdb

saveamberparm model ...prmtop ...inpcrd

amdpbd -p ...prmtop < ...inpcrd > ...pdb

With this pbd, the DOCK perl script prepare_amber.pl does not
interpret correctly the Hs at first LEU, adding a final extra H at the
end of the LEU residue (total 14Hs instead of 13) and being unable to
furnish pmrto/inpcrd for both the protein and the extra ligand. The
protein contains also a chloride ion ligand, which makes part of the
chains and seems to be treated OK (apart from vdw, which I don't know:
I use the default vdw in Amber ions param).

I nearly planned to try with Amber 9, if you encourage me to do so. I
must say (and posted) that with AmberTools 1.0/Antechamber I was
unable to get files for ligands, and had to do that with Amber 9. This
is why I have updated to AmberTools 1.2 (but I have not tried
Antechamber yet).

francesco

> 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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