Re: [AMBER] dna

From: case <>
Date: Mon, 28 Jun 2010 22:07:46 -0400

On Sun, Jun 27, 2010, wrote:

> i already sent the pdb file in earlier mail

You have to realize that on an email list, it can be difficult to track down
everything that was in an earlier message. I apologize if I missed something
from earlier on.

The key question is: does your input pdb file have phosphate groups on the
5' terminal residues? (see below)

> leaprc.ff99SB,i got following messege:
> dna1 = loadpdb oligo_p.pdb

It's also difficult to keep track of which version of amber you are using,
(again, apologies if this was in some earlier email.) If you are indeed
using AmberTools 1.4 (and are sure that your AMBERHOME variable is pointed
there, not to some earlier installation) you should not be seeing the hydrogen
atom naming problems reported below.

> Loading PDB file: ./oligo_p.pdb
> Created a new atom named: HO5' within residue: .R<DG 1>
> Created a new atom named: H5' within residue: .R<DG 1>
> Created a new atom named: H5'' within residue: .R<DG 1>
> Created a new atom named: H2' within residue: .R<DG 1>
> Created a new atom named: H2'' within residue: .R<DG 1>

Look in your $AMBERHOME/dat/leap/cmd/leaprc.ff99SB file. It should have
an addPdbAtomMap section with lines like this:

  { "H5'" "H5'1" }
  { "H5''" "H5'2" }
  { "HO2'" "HO'2" }
  { "HO5'" "H5T" }
  { "HO3'" "H3T" }

If it does not, you are not using the latest version of AmberTools.

> Added missing heavy atom: .R<DG 1>.A<P 1>
> Added missing heavy atom: .R<DG 1>.A<O1P 2>
> Added missing heavy atom: .R<DG 1>.A<O2P 3>

This is weird: do you want the terminal residue to be "DG" or "DG5"? Look
at the residue descriptions in $AMBERHOME/dat/leap/prep/

It looks to me(?) like your terminal residue in the PDB file does not have
a phosphate group.

> WARNING: There is a bond of 12.226016 angstroms between:
> ------- .R<DG 1>.A<O3' 33> and .R<DG 2>.A<P 1>

This looks like a serious problem. Is there indeed a long bond between
the O3' atom of residue 1 and P atom of residue 2? If so, your input PDB
file seems quite unsuitable. There are lots of such messages in the output,
and you need to find out what is going on.

You also need to learn how to compare your input pdb file to the library
residues referred to above, (taking into account the aliasing that goes on
in the leaprc file.)

Again, I apologize for having missed the earlier post where you provided the
pdb file. Maybe you should post it again, with a concise but exact
description of where it came from, and what version of AmberTools you are


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Received on Mon Jun 28 2010 - 19:30:03 PDT
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