Re: [AMBER] mismatch base pair from nab

From: Martina Devi <>
Date: Sat, 29 Aug 2015 05:39:10 -0700

Thank you to both of you sir. The matter was that I did not remove the
atoms that was not suppose to be there. So the pdb that was generated
should be edited with the atoms that should not be present in the modified


On Tue, Aug 25, 2015 at 12:57 PM, David A Case <>

> On Tue, Aug 25, 2015, Martina Devi wrote:
> >
> > I did not get any error message.The base which I did not edit can be
> viewed
> > in xleap The desired edited base which I want to load cannot be viewed in
> > xleap.
> Can you be more specific about what you mean by "cannot be viewed in
> xleap"?
> What were the exact commands you typed, and what was the exact response
> from
> the program?
> Don't restrict your reporting to what you think are "error messages". In
> order to help, we need to know everything that happened.
> >
> > What I did was I made two pdb files. Then I edited the required portion
> and
> > copied from the other pdb. Is this technique correct?
> Remember that you must remove any atoms in your modified residue that are
> not
> supposed to be there: all atoms present in the PDB file must also be in the
> library file for the modified residue.
> ....dac
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Received on Sat Aug 29 2015 - 06:00:03 PDT
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