From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Sep 17 2010 - 14:22:59 CDT
Are you using 0-based atom IDs in the extrabonds file? (If I recall
correcctly you should be.)
-Jim
On Sat, 4 Sep 2010, Kwee Hong wrote:
> Ya, it's the same.
>
> On Sat, Sep 4, 2010 at 5:41 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>wrote:
>
>> 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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