Re: [AMBER] help: MD on DNA

From: David A Case <case.biomaps.rutgers.edu>
Date: Thu, 2 Oct 2014 08:17:00 -0400

On Thu, Oct 02, 2014, pradeep pant wrote:
>
> DNA.pdb (which was downloaded from scfbio DNA Sequence to Structure tool)

> >Created a new atom named: 2H2 within residue: .R<DG 8>
> Created a new atom named: 1H5 within residue: .R<DC 9>
> Created a new atom named: 2H5 within residue: .R<DC 9>

....

The DNA.pdb file uses non-standard hydrogen names. I suggest that you
edit the file to remove these (I can't even figure out what names like
1H4 and 2H4 are likely to refer to), and look at the file visually to make
sure the rest looks OK. tleap will add hydrogens back in, with correct names.

...good luck...dac


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Received on Thu Oct 02 2014 - 05:30:02 PDT
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