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
REMARK 4 143D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
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
....dac
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Received on Tue Mar 16 2010 - 10:00:02 PDT
