Thank you very much. I have figured it out.
Li
On Tue, Jun 24, 2014 at 6:20 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Tue, Jun 24, 2014, 肖立 wrote:
>
> > Created a new atom named: 'H5' within residue: .R<RA 39>
> > Created a new atom named: 'HO2 within residue: .R<RA 39>
>
> Wow. Lots of things to suggest, even though you gave practically no
> information about which version of Amber you have, which leaprc file you
> used,
> where you got the PDB file from, etc.
>
> 1. It looks you are using an old PDB file: there are no longer residues
> named "RA" in Amber (they are just "A", etc., like in the PDB). It's
> recommended to update to the current version of AmberTools.
>
> 2. It looks(?) like the atom names for H5'' and HO2' in adenine residues
> are mangled. A simple thing is to just remove these, and let LEaP build
> them back in. Or, fix them in the PDB file: the atom names need to be in
> columns 13-16 of an ATOM card (with the "H" in column 13 if there are four
> characters in the name).
>
> ...good luck....dac
>
>
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>
--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Wed Jun 25 2014 - 10:30:02 PDT
