AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 14 2008 - 17:58:08 CDT

I did not try alternatives to ampdb from Amber9, which I can have with
a few commands, as this worked. The problem was not with leap. But
I'll try your suggestions once a fatal error with DOCK is solved. I
have posted the problem on dock_fans.
Thanks
francesco

On Tue, Oct 14, 2008 at 11:46 PM, Scott Brozell <sbrozell_at_scripps.edu> wrote:
> Hi,
>
> Have you tried all the various paths to leap-ophilic hydrogen names:
> Try using the -aatm option, eg,
> amdpbd -p ...prmtop -aatm < ...inpcrd > ...pdb
>
> Or using protonate to cleanup names and/or add hydrogens;
> see pp 251 in the amber10 manual.
> Or using reduce.
>
> Of course, it is common to strip hydrogens and let leap add them back.
>
> Scott
>
> On Tue, 14 Oct 2008, Francesco Pietra wrote:
>
>> Just to add that with Amber 9, LEU as first residue is treated correctly
>>
>> 1 N
>> 2 H1
>> 3 H2
>> 4 H3
>>
>> Therefore, I carried out a double check, using ambpdb with
>> inpcrd/prmtop gererated with Amber10. Result: what is faulty (at least
>> to this respect), is the module ambpdb in AmberTools 1.2, not xleap.
>>
>> This should be added to the bug I reported before for AmberTools (see
>> below, please).
>>
>> Whether this solves the problems with DOCK (I guuess are solved) is
>> another story, that I'll investigate.
>>
>> Cheers
>> francesco
>>
>>
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret_at_gmail.com>
>> Date: Tue, Oct 14, 2008 at 3:42 PM
>> Subject: Re: AMBER: LEaP problem with LEU first residue?
>> To: amber_at_scripps.edu
>>
>>
>> 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.
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