Re: [AMBER] Problem in Leap PDB Reading

From: David A Case <>
Date: Fri, 25 Oct 2019 12:09:18 -0400

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.


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Received on Fri Oct 25 2019 - 09:30:03 PDT
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