On Fri, Aug 26, 2011, vaibhav dixit wrote:
> I have used the following command in amber11 i.e. am1bcc in amber11 and bcc
> in amber10.
> But command with bcc is not successful due to convergence failure in
> amber11.
> [vaibhav.localhost VD69]$ antechamber -i VD69.pdb -fi pdb -o VD69_1.prep -fo
> prepi -c am1bcc -s 2
OK...what is happening is that antechamber doesn't recognize the "am1bcc"
flag, but doesn't give any error message. Hence, it doesn't calculate any
charges (all the charges in your prep file are zero). So, the program
finishes, but it doesn't "work" in any real sense.
(Volunteers are hereby solicited to get antechamber to emit appropriate
messages when it finds command line arguments it doesn't recognize.)
I don't know if you ever posted the VD69.pdb file that causes the problem with
sqm. It is sometimes that case that starting with a better initial geometry
(e.g. by minimizing in some other program like Gaussian) allows sqm to work.
But the more examples we have of lack of convergence in sqm, the more likely
it is that we can figure out what do to.
....dac
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Received on Fri Aug 26 2011 - 06:00:05 PDT
