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 Sun Aug 24 2014 - 04:30:02 PDT
