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
On 20 Jan 2012, at 14:46, kanika singal wrote:
> Dear AmberUsers,
>
> I have already sent this mail to the amber mail group before and resending
> it , since i have not received any reply. I am sorry if its a bothersome.
>
> I am building a Fe-metal centre. One of the ligands, CYS coordinates to FE
> using both SG and O atom. As a result I would NOT like to add terminal
> group such that it replaces the backbone with CH3. Thus I added the CH3
>
> group and capped the N terminal end using the following line.
>
> addFragment terminal/CH3 bd /NAME/MS2/CYF-2/.N.. ag /NAME/MS2/CYF-2/.CA. tr
> /NAME/MS2/CYF-2/.C.. 114.43
>
> However, this is giving the following error
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: addFragment
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: selection::parse ###
> ### Message: selection string = /1fx7_ms2/MS2/CYF-2/.N..
>
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: selection::parse ###
> ### Message: /col/mol/smol/atom selection error (7) ... exiting
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
>
> ### Function: MCPB::addFragment ###
> ### Message: Error in selection parsing ... exiting
> ### ### ### ###
>
> Can anyone please explain how to deal with such issues.
>
> Also, In the createBond part, would writing the following be correct
>
> createBond /NAME/MS2/FE2/FE.. /NAME/MS2/CYF/.SG.
> createBond /NAME/MS2/FE2/FE.. /NAME/MS2/CYF/.O..
>
> Thanks & Regards,
> Kanika
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 20 2012 - 08:00:03 PST
