Re: [AMBER] Problem in Leap PDB Reading

From: Yong Duan <duan.ucdavis.edu>
Date: Sun, 3 Nov 2019 23:07:38 +0000



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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Received on Sun Nov 03 2019 - 15:30:02 PST
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