AMBER Archive (2008)

Subject: Re: AMBER: Does LEaP understant capping with ACE/NME?

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 21 2008 - 12:31:36 CDT

While jogging I also thought my mistake in regard to leap was the
position of ACE. I'll move all ACE capping residues before their
respective protein residue and all NME after. If nothing more is
heard, it means it works.
Thanks for the suggestion
francesco

On Tue, Oct 21, 2008 at 6:02 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> 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_at_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
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu