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.gmail.com>
> Date: Tue, Oct 14, 2008 at 3:42 PM
> Subject: Re: AMBER: LEaP problem with LEU first residue?
> To: amber.scripps.edu
>
>
> On Tue, Oct 14, 2008 at 12:41 PM, Carlos Simmerling
> <carlos.simmerling.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.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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Received on Wed Oct 15 2008 - 05:11:49 PDT
