Hi Yuhui,
It seems that this is because of the naming of the atoms in the residue. Can you send me the input files
for this step? I can help to check them.
All the best,
Pengfei
On Aug 24, 2014, at 7:21 AM, Chris Gao <yuhuigao.mail.dlut.edu.cn> wrote:
> Thanks, Pengfei!
>
> I now successfully modify the sidechain.bcl file for my system but new questions come that:
>
> The metal Calcium in my protein's active site links with .O.. atom which is not on sidechain
>
> so, The sidechain.bcl is that:
>
> # Create bonds with Calcium
> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/AN1/.OD1
> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/VA1/.O.. (VA1=VAL)
> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/TR1/.O.. (TR1=TRP)
>
> that first line OD1 has no problem, but the last two containg .O.. atom in backbone. I check the bcl.log file, it says:
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: selection::parse ###
> ### Message: selection string = /2xjp/CLR/VA1/.O..
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: selection::parse ###
> ### Message: /col/mol/smol/atom selection error (7) ... exiting
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB::createBond ###
> ### Message: Error in selection parsing ... exiting
> ### ### ### ###
>
> It seems that sidechain.bcl only pocess metal interacts with sidechain??? Not atom in backbone??
>
>
> Thanks for your kind help!
>
> Yuhui
>
>
>
>> -----原始邮件-----
>> 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
>> 发送时间: 2014年8月23日 星期六
>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>> 抄送:
>> 主题: Re: [AMBER] MCPB and sidechain.bcl problem
>>
>> Hi Yuhui,
>>
>> On Aug 22, 2014, at 8:55 AM, 高彧辉 <yuhuigao.mail.dlut.edu.cn> wrote:
>>
>>> Hi .all!
>>>
>>> I have some difficulties in MCPB.
>>>
>>> 1st): I edit original my pdb file end run
>>> MCPB 1234_addHs.bcl -l 1234_addHs.bcl.log
>>> but occurs Error: 1 Error in watProtonate ... exiting
>>> terminate called after throwing an instance of 'MTKpp::MTKException'
>>> Aborted (core dumped)
>>>
>>> Then I use tleap to add H
>>>
>>
>> That is right. MCPB may met problem when adding the hydrogens on water. Other tools could be used at this situation.
>>
>>> 2nd): the 1AMP_OH_sidechain.bcl in tutorial generated manually has no explanation about syntax and meaning in detail,
>>> I don't know how to modify the bcl file precisely for my own system.
>>>
>>> Like a sentence:
>>>
>>> addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr /NAME/CLR/HD1-1/.ND1 87.0
>>>
>>> what does the sentence mean and 87.0 stand for??
>>
>> In this example we used the methyl group to replace the CA atom in the backbone.
>> 87.0 is the dihedral values between the CA, CB, CG and ND1 atoms of that residue in the original PDB file.
>> (If you met a negative dihedral value in PDB, you need to change it to positive by adding 360 degree in the MCPB script.)
>> The dihedral values may be different for different residues, you need to check them manually before setting them in the script.
>>
>>>
>>> I sincerely hope someone can help me!
>>>
>>
>> Sorry for that there is no notes for that part, I will add notes in that part in the corresponding file in that tutorial.
>>
>>> Thanks
>>
>> No problem.
>>
>> All the best,
>> Pengfei
>>
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Received on Mon Aug 25 2014 - 06:30:02 PDT
