have you searched the archives? I did, using the message you lsit below
"Created a new atom named H5 ' within residue" and found lots of
information. that might be a good place to start while you wait for other
replies.
On Tue, Mar 16, 2010 at 9:08 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> 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.
> In xleap, the commands are:
>
> >dna=loadpdb "path/143d.pdb"
>
> >Created a new atom named H5 ' within residue: .R<DA 1>
> >Created a new atom named H5 ' ' within residue: .R<DA 1>
> ......
>
> >saveamberparm dna 143d_vac,prmtop 143d_vac.inpcrd
>
> .....
> FATAL Atom .R<DA 1>.A<H5' 33>does not have a type.
> FATAL Atom .R<DA 1>.A<H5'' 34>does not have a type.
> FATAL Atom .R<DA 1>.A<HO'5 37> does not have a type.
> FATAL Atom .R<DG 4>.A<H2' 36>does not have a type.
> FATAL Atom .R<DG 4>.A<H2'' 37>does not have a type.
> ........
> Failed to generate parameters
> Parameter file was not saved
>
> Completely confused what to do....Please help.
>
> Thanks,
> Asfa.
>
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Received on Tue Mar 16 2010 - 06:30:05 PDT
