Hello Vishal
The hydrogen atom bonded to N1 of the guanine bases has the wrong
name. In your file is like '1H'
Switch it to 'H1' and it will work. I tested it and is now compatible
with the definitions.
Hope that helps!
Rodrigo.
On Mon, Sep 29, 2014 at 7:38 AM, Vishal Nemaysh
<vishal.bioinfotech.gmail.com> wrote:
> *Dear all, I am getting a error leap when i prepare the .prmtop & .inpcrd
> files. How to resolve it? the pdb file is also attached herewith. Thanks in
> advance*
>
>
> *> saveamberparm dna dna_wat.prmtop dna_wat.inpcrd*
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -23.000000 is not zero.
> FATAL: Atom .R<DG5 1>.A<H 32> does not have a type.
> FATAL: Atom .R<DG 4>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 7>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 10>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 13>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 16>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 19>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 22>.A<H 34> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> --
> Vishal
> Research Scholar,
> Neuropharmaceutical Chemistry lab.,
> Dr. B. R. Ambedkar Center for Biomedical Research,
> University of Delhi, Delhi-110007
> Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> Phone: 91-11-27662778 Mobile: 91+9650736653
>
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Received on Mon Sep 29 2014 - 08:00:02 PDT
