AMBER Archive (2007)

Subject: Re: AMBER: Torsion terms in xleap

From: Lili Peng (lilipeng_at_gmail.com)
Date: Wed Sep 19 2007 - 13:41:14 CDT

Dear Dr. Case and others,

I think Junmei has brought up this issue before - that my structure is "not
good enough." This leaves me to question what defines a structure as "good"
or "bad"? If geometry is the only issue, what approach should I take to
create a structure that has a good (or better) geometry? Basically, my
question is: in creating an initial structure, what features should I be
aware of to ensure that my structure is "good enough"?

Thanks,
Lili

On 9/17/07, David A. Case <case_at_scripps.edu> wrote:
>
> On Mon, Sep 17, 2007, Lili Peng wrote:
> >
> > My apologies for the repeat question :). However, I did try to do the
> > "pre-processing" of the mol2 file in antechamber before I sent the
> original
> > email, but I ran into a problem with loading the prepi file in xleap.
>
> As Junmei has explained, the problem lies in the fact that your starting
> geometry is just bad enough that antechamber mis-assigns bonds. Junmei's
> workaround does not appear to have worked for you, and I don't have any
> practical suggestions other than: get a better starting structure.
>
> > x = loadamberprep glu4_linear_PTX.prepi
>
> This is not the correct syntax: type "help loadAmberPrep" at the LEaP
> prompt.
>
> But that won't solve your structure problem....
>
> ...dac
>
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