Re: [AMBER] Errors during Building Sidechain Model(MCPB program)

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Sat, 17 Jan 2015 10:37:44 -0500

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>_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



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Received on Sat Jan 17 2015 - 08:00:03 PST
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