Re: [AMBER] Problem in Leap PDB Reading

From: Yong Duan <duan.ucdavis.edu>
Date: Wed, 6 Nov 2019 05:48:40 +0000


Well, don't be too hard on yourself. The way I see it is that it reminds us to choose A copy as the default in leap so that users don't keep tripping on this sort of mundane issues.

yd

´╗┐On 11/3/19, 4:31 PM, "Robert Molt" <rwmolt07.gmail.com> wrote:

    Thank you; I apologize for missing such an obvious issue, as a neophyte
    with pdb s.
    
    On 11/3/19 6:07 PM, Yong Duan wrote:
>
> Hi Robert,
>
> Column 17 of atoms 4503 - 4604 indicate A and B two copies. You need to remove one copy.
>
> yd
>
> On 11/3/19, 2:26 PM, "Robert Molt" <rwmolt07.gmail.com> wrote:
>
> Good evening,
>
> I confirm that I attached the file in the original email I sent to the
> Amber list-serv. It seems that it gets scrubbed? Is this one going through?
>
> On 10/25/19 12:09 PM, David A Case wrote:
> > On Wed, Oct 23, 2019, Robert Molt wrote:
> >> System under consideration: I have a system with both a protein and a
> >> DNA helix. I have amino acids numbered 43-318; I then have nucleic acids
> >> numbered 1-21, twice (once for each strand). I have attached the relevant
> >> PDB file in this email.
> > I don't see any attachment.
> >
> >> In particular, the amino acids are numbered
> >> 43-318 in the file, and then the nucleic acids are numbered 1-21 for the
> >> first strand, then 1-21 again for the second strand.
> > Be sure you have TER cards between separate chains.
> >
> >> -- residue 328: duplicate [ C1'] atoms (total 2)
> > This is a pretty specific message: are you sure you don't have two C1'
> > atoms in any of the nulceic acid residues? The "328" looks odd, since,
> > by my count, you should have only 318 total residues.
> >
> > There probably aren't that many C1' atoms in the entire PDB file: look
> > at all of them for anything that looks funny.
> >
> >> 1.) Should numbering in a pdb file for leap be consecutive? i.e., 43-360, in my case?
> > No, that is not required.
> >
> >> Created a new atom named: N1 within residue: .R<OMC 328>
> > This means that you have an atom named N1 in the OMC residue, but there
> > is no such atom in the library file that defines OMC. (Did you load
> > an OMC unit?
> >
> > Usual debugging strategy: edit down the PDB file to smaller parts, and
> > try loading into tleap. Is the protein only OK? Then add a small bit
> > of DNA. Maybe everything except the OMC part. etc.
> >
> > ...dac
> >
> >
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>
> --
> Dr. Robert Molt Jr.
>
>
>
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    --
    Dr. Robert Molt Jr.
    
    
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Received on Tue Nov 05 2019 - 22:00:03 PST
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