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
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Received on Fri Jan 20 2012 - 07:00:03 PST
