Glad you could get it sorted. Thanks for letting us know.
Ben
On 22/01/2012, at 2:26 AM, kanika singal <singalkanika1.gmail.com> wrote:
> Dear Peter,
>
> Sorry for all the trouble. I have solved the issue. I realised that while
> adding the residue CYS in the cluster I was using 'not bb' and as a result
> MCPB could not find the carbonyl oxygen. Its working fine now.
>
> Thanks & Regards
> Kanika
>
> On Sat, Jan 21, 2012 at 3:48 PM, kanika singal <singalkanika1.gmail.com>wrote:
>
>> Dear Peter,
>>
>> Please find the necessary files attached.
>>
>> 1. 1fx7_ms2_fixed.pdb
>> 2. 1fx7-ms2_settings.bcl
>> 3. 1fx7_ms2_sidechain.bcl (this file has the problem)
>> 4. 1fx7_ms2_sidechain.bcl.log (this is the log file with the error)
>>
>> I hope i have sent you all the necessary files. Please ask me if you need
>> some other files. Would be glad to help.
>>
>> I am sure I have applied all the bug fixes as i have recently solved one
>> metal centre with MCPB without any error. In this case the problem is due
>> to coordination bond of carbonyl oxygen of Cys with the metal. As a result
>> I cannot cap the complete backbone as is usually done. Thus I am trying o
>> cap N terminal of CYS with NME, which is giving error.
>>
>> Thanks and Regards
>> Kanika
>>
>> PS: I am resending the mail as the earlier mail bounced back and it wanted
>> approval from the moderator due to big subject line. Sorry for the spam.
>>> Hi Kanika,
>>>
>>> I will need you to send me all the necessary files to reproduce the
>> problem on
>>> my machine. Also, make sure you are have applied all bug fixes to
>> AmberTools.
>>>
>>> Regards,
>>> Martin
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Received on Mon Jan 23 2012 - 12:30:02 PST
