Re: [AMBER] regarding NMR structures

From: case <>
Date: Tue, 16 Mar 2010 12:41:28 -0400

On Tue, Mar 16, 2010, Asfa Ali wrote:
> I am working on the G-quadruplex DNA (PDB ID-*143D*) and the NMR structure
> was published in 1993 and AMBER 9 was released on March, 2006. But still it
> is not able to create the prmtop and inpcrd files.

If you examine the 143D.pdb file you will see lines like this:

REVDAT 3 24-FEB-09 143D 1 VERSN


This indicates that the atom and residue nomenclature for this entry were
updated to version 3 in Feb. 09.

By far the simplest thing to do is just to download and install the current
version of AmberTools. Here is what I get:

tleap -f leaprc.ff99bsc0
> x = loadpdb 143D.pdb
Loading PDB file: ./143D.pdb
  total atoms in file: 4290
> saveAmberParm x prmtop prmcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -126.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 768 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit


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Received on Tue Mar 16 2010 - 10:00:02 PDT
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