AMBER Archive (2008)

Subject: Re: AMBER: Tough time with antechamber

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 24 2008 - 20:25:33 CST

On Thu, Jan 24, 2008, Junmei Wang wrote:

> It is a good idea to write out the optimized structure in pdb format when
> the output format is -gout or divout or charge method is bcc or mul or cm1
> or cm2. I would like to call it divcon.pdb and mopac.pdb.

Sounds like a good idea.

> But if the starting geometry is really bad, I suspect AM1 or PM3
> optimization always produces sound structure.

Of course, users should be encouraged to examine the optimized structures to
make sure that they make sense.

>
> In AMBER10, the newly introduced program, acdoctor can help users to detect
> lots of input problem. For this particular case, acdoctor finds that there
> are more than one unit (since HD is isolated from the other atoms) and
> prints out an error message.

We need to update the examples and tutorials to get people to know about
acdoctor. Otherwise, it is likely to be unused.

...thx...dave
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