AMBER Archive (2006)

Subject: Re: AMBER: optimatized structure is so much different from the original pdb structure

From: Gabbar S. Daaku (gabbarsinghdaaku_at_gmail.com)
Date: Fri Nov 17 2006 - 11:13:04 CST

Hi Emilia,

You did not provide information on what the conformational change is
due to, however, since you mention that "it turns over from one side
to the other" it appears that it might be due to dihedral angle(s)
going from one minima to another. You should use look at the example
where charge for molecules with multiple conformations are calculated.
See 0README file in $AMBERHOME/examples/resp_charge_fit and look at
the following example: bis-napthyl One molecule with a two stage
fit on two conformations

GSD

On 11/17/06, emilia wu <emiliawu_at_dicp.ac.cn> wrote:
> hi,all
>
> I am doing some calculation about the binding between inhibitor and protein, and I use Gaussian to
> get the charge parameters of inhibitor with resp fitting. after the optimization with HF/6-31G**, I got a
> conformation which is so different from the origianl conformation from the protein data bank that
> it turn over from one side to the other. I just want to know whether we can use this Gaussian log file
> to get the prepi file for calculating the binding energy. does it matter to the later calculation?
> thanks in advance!
>
>
>
>
> emilia
> emiliawu_at_dicp.ac.cn
> 2006-11-17
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