AMBER Archive (2007)

Subject: Re: AMBER: problems in adding ACE and NME group

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jun 20 2007 - 23:28:30 CDT

it would help if you provide leap input/output. is there any error or
warning?

On 6/21/07, backy <backy_at_ibms.sinica.edu.tw> wrote:
>
> by the way, this complete protein is a test case for me practicing the
> protein capping stuff.
> :)
> backy
>
> ----- Original Message -----
> From: "backy" <backy_at_ibms.sinica.edu.tw>
> To: <amber_at_scripps.edu>
> Sent: Thursday, June 21, 2007 11:54 AM
> Subject: Re: AMBER: problems in adding ACE and NME group
>
>
> > If there is a need in placing the whole ACE and NME group, how should I
> > input their initial coordinations?
> > Thanks.
> >
> > backy
> >
> >
> >
> >
> > ----- Original Message -----
> > From: "David A. Case" <case_at_scripps.edu>
> > To: <amber_at_scripps.edu>
> > Sent: Wednesday, June 20, 2007 11:41 PM
> > Subject: Re: AMBER: problems in adding ACE and NME group
> >
> >
> >> On Wed, Jun 20, 2007, backy wrote:
> >>
> >>> Parameter file was not saved.
> >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> >>
> >> You had error in the leap step, never actually made a prmtop file.
> >>
> >>>
> >>> ATOM 1 C ACE A 1 70.110 65.868 39.946 1.00 0.00
> >>> ATOM 2 CA ALA A 1 70.537 66.473 38.657 1.00 0.00
> >>> ATOM 3 C ALA A 1 69.639 67.664 38.316 1.00 0.00
> >>> ATOM 4 O ALA A 1 68.434 67.654 38.604 1.00 0.00
> >>> ATOM 5 CB ALA A 1 70.456 65.436 37.551 1.00 0.00
> >>> ATOM 6 N THR A 2 70.232 68.687 37.711 1.00 0.00
> >>> ATOM 7 CA THR A 2 69.495 69.875 37.320 1.00
> 0.00
> >>> ATOM 8 C THR A 2 69.540 70.004 35.797 1.00 0.00
> >>
> >> You have to add an entire ACE residue (or at least the heavy atoms),
> not
> >> just
> >> one C atom. Also, you have two residues labelled "1" (ACE and ALA),
> >> which
> >> will confuse LEaP. Also, there is no N atom for the ALA.
> >>
> >> Don't try to run sander until you get LEaP running the way it should.
> >>
> >> ...good luck...dac
> >>
> >> p.s.: are you sure you want to add the capping groups to a complete
> >> protein?
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> >>
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> >> Version: 7.5.472 / Virus Database: 269.9.1/854 - Release Date:
> 2007/6/19
> >> ¤U¤È 01:12
> >>
> >>
> >
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> >
>
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