[AMBER] regarding NMR structures

From: Asfa Ali <asfa.iisc.gmail.com>
Date: Tue, 16 Mar 2010 18:38:20 +0530

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 - 06:30:03 PDT
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