Hi Wenjuan,
On Jan 14, 2015, at 11:18 PM, wjli <wenjuanli93.gmail.com> wrote:
> Dear Amber members,
>
> I have created metal ion force field（containing one CU）successfully.This time ,I need to build force field with three copper ions.
> During the Building Sidechain Model step,following errors:happened:
> 1.### ### ### ###
> ### MTK++ Error ###
> ### Function: connections::assignStdAngles ###
> ### Message: Please assign angles before assigning MM parameters for molecule: CU
> ### ### ### ###
>
For this step, I think it is a problem met during adding the hydrogens. You can add the hydrogen first by using another tool
and then based on that step to do the following modeling. I have changed that part in the script attached.
> 2.### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: createResidue
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: MCPB ###
> ### Message: addToResidue
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: selection::parse ###
> ### Message: selection string = /lac_3CU/CLR/CU2
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: selection::parse ###
> ### Message: selection string = /lac_3CU/3/.CU-503/CU..
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: selection::parse ###
> ### Message: /col/mol/smol/atom selection error (6) ... exiting
> ### ### ### ###
>
> I think my selection grammar have no problem.You can find my sidechain.bcl in the attachment.
>
In the script you have:
# Create CU2-13 from CU-503
createResidue CU2 in CLR
addToResidue /NAME/CLR/CU2 /NAME/3/.CU-503/CU..
# Create CU3-14 from CU-501
createResidue CU3 in CLR
addToResidue /NAME/CLR/CU3 /NAME/4/.CU-501/CU..
# Create CU4-15 from CU-502
createResidue CU4 in CLR
addToResidue /NAME/CLR/CU4 /NAME/5/.CU-502/CU..
From my experience, this may be because that you have used the wrong atom number here.
For CU2, you used NAME/3/.CU-503 but for CU3, you used NAME/4/.CU-501.
It suggest it to be:
# Create CU2-13 from CU-503
createResidue CU2 in CLR
addToResidue /NAME/CLR/CU2 /NAME/3/.CU-501/CU..
# Create CU3-14 from CU-501
createResidue CU3 in CLR
addToResidue /NAME/CLR/CU3 /NAME/4/.CU-502/CU..
# Create CU4-15 from CU-502
createResidue CU4 in CLR
addToResidue /NAME/CLR/CU4 /NAME/5/.CU-503/CU..
I have changed the related part in the input file and attached it here.
Please check it and let me know whether it works.
Hope that helps,
Pengfei
> I look forward to your reply!
> wjli<lac_3CU_sidechain.bcl>_______________________________________________
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Received on Sat Jan 17 2015 - 08:00:03 PST
