Re: Bad atom ID in extra bond file

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Sat Sep 04 2010 - 04:41:00 CDT

Hi,

On Sat, Sep 4, 2010 at 10:10 AM, Kwee Hong <joyssstan0202_at_gmail.com> wrote:
> Hi,
>
> I was trying to minimize my protein in vacuum. In my config file, I included
> an extra bond file which its content is as follow:
>
> angle 385 292 387 92 120
> angle 387  88 386 92 120
> angle 386 173 385 92 120
>
> I don't understand the reason I got this fatal message when I tried to
> minimized it:
>
> Charm++ fatal error:
> FATAL ERROR: BAD ATOM ID IN EXTRA BONDS FILE extraAngles.txt: angle 385 292
> 387 92 120
>
> It worked ok when I minimized this protein in a water box with the same
> extra bond file. Can anyone tell me why?

Are you sure these atoms have the same index in both of your systems
(vacuo and solvent)?

Cheers,
Leo

> And can anyone tell me where can i get tutorial on simulating protein in
> vacuum?
>
> Thanks.
>
> Regards,
> Joycw
>

--
Leonardo Trabuco, Ph.D.
CellNetworks, BioQuant
University of Heidelberg, Germany

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