Bad atom ID in extra bond file

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Sat Sep 04 2010 - 03:10:25 CDT

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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?

And can anyone tell me where can i get tutorial on simulating protein in
vacuum?

Thanks.

Regards,
Joycw

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