Re: [AMBER] problem to generate parameters files of DNA

From: case <>
Date: Wed, 10 Mar 2010 08:09:47 -0500

On Wed, Mar 10, 2010, Ananya Paul wrote:

> I am facing the problem to generate parameters files. I have made dimeric
> sequence from one monomeric PDB ID, in pymol software. After generating this
> when I am preparing parameters files(.prmtop, .inpcrd) It is showing
> following Error. I am attaching the PDB of my DNA.
> FATAL: Atom .R<DG 2>.A<P10 34> does not have a type.
> FATAL: Atom .R<DG 2>.A<O20 35> does not have a type.

Atom and residue names in PDB files must match those in the Amber libraries.
Amber knows about "DG" (deoxy-guanosine), but the atom naming convention
you (or pymol) is using is nonstandard. Amber uses atom names from the PDB,
which do not include things like "P10" or "O20". You will have to construct
your pdb file (or edit it) so that the correct atom names are used.


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Received on Wed Mar 10 2010 - 05:30:03 PST
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