Hi Kanika,
On 18/01/2012, at 1:50 AM, kanika singal wrote:
> Dear AmberUsers,
>
> 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.
This looks like a syntax error in your selection string. Martin, are you able to clarify what the correct syntax is? I can't remember off the top of my head.
> 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..
This looks OK to me.
Regards,
Ben
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Received on Sat Jan 21 2012 - 10:00:03 PST
