From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Sat Sep 04 2010 - 05:08:03 CDT
Ya, it's the same.
On Sat, Sep 4, 2010 at 5:41 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>wrote:
> On Sat, Sep 4, 2010 at 10:10 AM, Kwee Hong <joyssstan0202_at_gmail.com>
> > Hi,
> > I was trying to minimize my protein in vacuum. In my config file, I
> > 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
> > 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)?
> > 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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