it looks like you've put the ACE after the protein- I don't think Leap
could understand that you want it moved to the start.
if you put the ACE before the Leu 1 and change HETATM to ATOM it
should work fine.
On Tue, Oct 21, 2008 at 11:57 AM, Francesco Pietra
<chiendarret.gmail.com> wrote:
> Hi:
>
> For reasons that would be long to detail, I would like to work
> (Amber10) with a model where the first and last residues are capped
> with ACE and NME respectively. That for more than one stretch of
> standard amino acids. The stretches are separated from one another by
> a TER line
>
> The way I have built the pdb file is not undestood by leap.
>
> As an example with one stretch, the first amino acid:
>
> ATOM 1 N LEU 1 xyz
> ATOM 2 CA LEU 1
> ATOM 3 CB LEU 1
> ATOM 4 CG LEU 1
> ATOM 5 CD1 LEU 1
> ATOM 6 CD2 LEU 1
> ATOM 7 C LEU 1
> ATOM 8 O LEU 1
> ATOM 9 HA LEU 1
> ATOM 10 HB2 LEU 1
> ATOM 11 HB3 LEU 1
> ATOM 12 HG LEU 1
> ATOM 13 HD11 LEU 1
> ATOM 14 HD12 LEU 1
> ATOM 15 HD13 LEU 1
> ATOM 16 HD21 LEU 1
> ATOM 17 HD22 LEU 1
> ATOM 18 HD23 LEU 1
> ATOM 19 H LEU 1
>
> The corresponding ACE:
>
> HETATM 4018 C ACE 46 xyz
> HETATM 4019 O ACE 46
> HETATM 4020 CH3 ACE 46
> HETATM 4021 HH31 ACE 46
> HETATM 4022 HH32 ACE 46
> HETATM 4023 HH33 ACE 46
>
> The various capping residues are NOT separated from one another by a TER line.
>
> LEaP does not understand that there is capping (while Chimera
> understands that and reproduces perfectly the whole structure). LEaP
> adds a new atom, named H, to each beginning terminal, and "missing"
> OXT to each terminal last. Then it tries to join first ACE with last
> NME. Perhaps I could avoid the last issue by placing a TER line
> between the capping residues but before embarking in a perhaps
> hopeless avenue, I ask for experience, or insight.
>
> Without capping, the model is treated correctly by LEaP, though it has
> charges that the true protein has not, which does not fit my plans.
>
> Thanks
> francesco pietra
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Received on Wed Oct 22 2008 - 05:10:38 PDT
