Hi Yuhui,
I checked the input file. You could not choose the backbone oxygen is because you did not
include the backbone in the sidechain model. : ) It is the normal situation that you don't
need to consider the backbone atoms, but since there are backbone atoms coordinated to the metal
ion, you need to consider it apparently.
I have changed the input file a little bit. Take the backbone of VAL and TRP into consideration.
Then I used the CH3 group to capped the backbone in two directions.
I used the 2xjp_fixed_H.pdb file directly, so there is some residue number changes in the input file.
Here is the input file after modification.
Meanwhile, you can try the nonbonded model to simulate the Ca2+ ion since there is usually not very strong
coordinated bond between the Ca ion and the surrounding residues.
You can check the following paper if interested.
http://pubs.acs.org/doi/abs/10.1021/ct400146w
Hope it helps,
Pengfei
On Aug 25, 2014, at 11:32 PM, Chris Gao <yuhuigao.mail.dlut.edu.cn> wrote:
> Thank you for your help, Pengfei!
>
> I send a .tar file containing my pdb file, bcl file and README with detail information about my protein and my question!
>
>
> I hope this do not bother to you！
>
> Best,
> Gao
>
>> -----原始邮件-----
>> 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
>> 发送时间: 2014年8月25日 星期一
>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>> 抄送:
>> 主题: Re: [AMBER] MCPB and sidechain.bcl problem
>>
>> 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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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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Received on Tue Aug 26 2014 - 12:30:03 PDT
