Re: [AMBER] unexpected behavior of ambpdb

From: Brian Radak <radak004.umn.edu>
Date: Fri, 3 Jun 2011 13:15:40 -0400

Thank you. I figured there was some sensible reason for what I was seeing.
That is a much more elegant and portable solution than my idea of running
sed every time I made a pdb :P


On Fri, Jun 3, 2011 at 12:54 PM, David A Case <case.biomaps.rutgers.edu>wrote:

>
> On Jun 3, 2011, at 11:16 AM, Brian Radak <radak004.umn.edu> wrote:
> >
> > O1P --> OP1
> > O2P --> OP2
>
> ambpdb is trying to make atom names compatible with pdb version 3, so that
> prmtop files created before ff10 for nucleic acids would have the proper
> names.
>
> You can turn off the name conversion with the -aatm flag, as I recall.
>
> ...dac
>
> >
>
>
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Received on Fri Jun 03 2011 - 10:30:03 PDT