Re: [AMBER] MCPB and sidechain.bcl problem

From: Chris Gao <yuhuigao.mail.dlut.edu.cn>
Date: Tue, 26 Aug 2014 11:32:23 +0800 (GMT+08:00)

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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Received on Mon Aug 25 2014 - 21:00:02 PDT
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