[AMBER] MCPB : addFragment in case of CYM

From: kanika singal <singalkanika1.gmail.com>
Date: Wed, 18 Jan 2012 12:20:08 +0530

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.

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
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Received on Tue Jan 17 2012 - 23:00:02 PST
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