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 Sat Jan 21 2012 - 23:30:03 PST
