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

From: Ananya Paul <>
Date: Wed, 10 Mar 2010 20:07:40 +0530

Dear Sir,
Thank you for your suggestion, I have tried to change the naming, but it is
not forming, please help me to generate the new pdb by changing the name of
the atom.
With Regards

On Wed, Mar 10, 2010 at 6:39 PM, case <> wrote:

> 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.
> ...dac
> _______________________________________________
> AMBER mailing list

Ananya Paul
Senior Research Fellow
Dept. of Organic Chemistry
Indian Institute of Science, Bangalore
AMBER mailing list
Received on Wed Mar 10 2010 - 07:00:03 PST
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